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annotate alchemical_run/test-data/Report.txt @ 0:19d1d4c30402 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
author chemteam
date Mon, 11 Nov 2019 13:20:39 -0500
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19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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1 Starting minimization for lambda = 0...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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2 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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3
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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4 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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5 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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6 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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7 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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8 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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9 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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10 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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11 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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12 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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13 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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14 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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15 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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16 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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17 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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18
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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19 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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20 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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21 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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22 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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23 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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24
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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25 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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26 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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27 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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28 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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29
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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30 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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31 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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32 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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33 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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34 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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35 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_0.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min0.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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36
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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37 Setting the LD random seed to -127141127
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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38 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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39 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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40 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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41 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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42 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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43 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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44 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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45 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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46 Number of degrees of freedom in T-Coupling group rest is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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47 Estimate for the relative computational load of the PME mesh part: 0.21
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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48
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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49 GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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50
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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51 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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52 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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53 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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54 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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55 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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56 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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57 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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58 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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59 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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60 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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61
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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62 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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63 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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64 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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65 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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66 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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67 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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68 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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69 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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70 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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71 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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72 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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73 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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74 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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75 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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76
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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77 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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78 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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79 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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80 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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81 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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82
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83 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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84 under the terms of the GNU Lesser General Public License
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85 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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86 of the License, or (at your option) any later version.
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87
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88 GROMACS: gmx mdrun, version 2019.1
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89 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
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90 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
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91 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM
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92 Command line:
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93 gmx mdrun -deffnm min0
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94
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95 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
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96 The current CPU can measure timings more accurately than the code in
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97 gmx mdrun was configured to use. This might affect your simulation
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98 speed as accurate timings are needed for load-balancing.
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99 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
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100 Reading file min0.tpr, VERSION 2019.1 (single precision)
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101
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102 Using 1 MPI thread
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103 Using 4 OpenMP threads
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104
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105
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106 Steepest Descents:
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107 Tolerance (Fmax) = 1.00000e+02
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108 Number of steps = 10
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109
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110 Energy minimization reached the maximum number of steps before the forces
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111 reached the requested precision Fmax < 100.
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112
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113 writing lowest energy coordinates.
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114
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115 Steepest Descents did not converge to Fmax < 100 in 11 steps.
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116 Potential Energy = -8.3125391e+04
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117 Maximum force = 2.1372287e+04 on atom 1
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118 Norm of force = 5.1859150e+02
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119
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120 GROMACS reminds you: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." (Watson & Crick)
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121
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122 Starting constant volume equilibration...
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123 :-) GROMACS - gmx grompp, 2019.1 (-:
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124
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125 GROMACS is written by:
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126 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
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127 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
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128 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
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129 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
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130 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
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131 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
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132 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
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133 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
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134 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
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135 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
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136 Christian Wennberg Maarten Wolf
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137 and the project leaders:
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138 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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139
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140 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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141 Copyright (c) 2001-2018, The GROMACS development team at
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142 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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143 the Royal Institute of Technology, Sweden.
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144 check out http://www.gromacs.org for more information.
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145
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146 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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147 under the terms of the GNU Lesser General Public License
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148 as published by the Free Software Foundation; either version 2.1
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149 of the License, or (at your option) any later version.
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150
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151 GROMACS: gmx grompp, version 2019.1
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152 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
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153 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
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154 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT
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155 Command line:
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156 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_0.mdp -c ../EM/min0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt0.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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157
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158 Setting the LD random seed to -187712966
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159 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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160 Generating 1-4 interactions: fudge = 0.5
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161 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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162 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
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163 Excluding 3 bonded neighbours molecule type 'NA'
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164 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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165 Excluding 3 bonded neighbours molecule type 'WAT'
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166 Velocities were taken from a Maxwell distribution at 300 K
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167 Removing all charge groups because cutoff-scheme=Verlet
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168
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169 NOTE 1 [file morph.top, line 232]:
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170 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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171 an estimated oscillational period of 8.0e-03 ps, which is less than 10
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172 times the time step of 1.0e-03 ps.
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173 Maybe you forgot to change the constraints mdp option.
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174
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175 Number of degrees of freedom in T-Coupling group System is 12987.00
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176 Estimate for the relative computational load of the PME mesh part: 0.23
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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177
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178 There was 1 note
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179
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180 GROMACS reminds you: "Nada e organico, e tudo programado" (Pitty)
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181
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182 Analysing residue names:
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183 There are: 1 Other residues
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184 There are: 10 Ion residues
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185 There are: 2151 Water residues
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186 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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187 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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188 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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189 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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190 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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191 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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192 Calculating fourier grid dimensions for X Y Z
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193 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
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194 This run will generate roughly 1 Mb of data
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195 :-) GROMACS - gmx mdrun, 2019.1 (-:
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196
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197 GROMACS is written by:
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198 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
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199 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
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200 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
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201 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
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202 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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203 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
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204 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
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205 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
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206 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
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207 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
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208 Christian Wennberg Maarten Wolf
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209 and the project leaders:
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210 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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211
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212 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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213 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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214 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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215 the Royal Institute of Technology, Sweden.
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216 check out http://www.gromacs.org for more information.
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217
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218 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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219 under the terms of the GNU Lesser General Public License
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220 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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221 of the License, or (at your option) any later version.
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222
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223 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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224 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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225 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
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226 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT
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227 Command line:
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228 gmx mdrun -deffnm nvt0
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229
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230 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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231 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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232 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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233 speed as accurate timings are needed for load-balancing.
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234 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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235 Reading file nvt0.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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236 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
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237
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238
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239 Using 1 MPI thread
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240 Using 4 OpenMP threads
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241
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242 starting mdrun 'BioSimSpace System'
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243 50 steps, 0.1 ps.
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244
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245 Writing final coordinates.
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246
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247 Core t (s) Wall t (s) (%)
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248 Time: 1.458 0.365 399.9
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249 (ns/day) (hour/ns)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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250 Performance: 12.084 1.986
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251
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252 GROMACS reminds you: "I Quit My Job Blowing Leaves" (Beck)
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253
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254 Constant volume equilibration complete.
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255 Starting constant pressure equilibration...
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256 :-) GROMACS - gmx grompp, 2019.1 (-:
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257
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258 GROMACS is written by:
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259 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
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260 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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261 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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262 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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263 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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264 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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265 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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266 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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267 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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268 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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269 Christian Wennberg Maarten Wolf
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270 and the project leaders:
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271 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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272
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273 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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274 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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275 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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276 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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277 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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278
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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279 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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280 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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281 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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282 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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283
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284 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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285 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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286 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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287 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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288 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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289 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_0.mdp -c ../NVT/nvt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt0.cpt -o npt0.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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290
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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291 Setting the LD random seed to 2038796930
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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292 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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293 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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294 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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295 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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296 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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297 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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298 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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299 Removing all charge groups because cutoff-scheme=Verlet
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300
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301 NOTE 1 [file morph.top, line 232]:
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302 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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303 an estimated oscillational period of 8.0e-03 ps, which is less than 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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304 times the time step of 1.0e-03 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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305 Maybe you forgot to change the constraints mdp option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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306
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307 Number of degrees of freedom in T-Coupling group System is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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308 Reading Coordinates, Velocities and Box size from old trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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309 Will read whole trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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310 Last frame -1 time 0.050
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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311 Using frame at t = 0.05 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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312 Starting time for run is 0 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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313 Estimate for the relative computational load of the PME mesh part: 0.23
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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314
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315 There was 1 note
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316
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317 GROMACS reminds you: "Act like Prometheus would" (Gogol Bordello)
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318
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319 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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320 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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321 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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322 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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323 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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324 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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325 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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326 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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327 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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328 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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329 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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330 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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331 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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332 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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333
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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334 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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335 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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336 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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337 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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338 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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339 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
340 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
341 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
342 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
343 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
344 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
345 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
346 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
347 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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348
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
349 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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350 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
351 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
352 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
353 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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354
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
355 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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356 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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357 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
358 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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359
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
360 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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361 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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362 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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363 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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364 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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365 gmx mdrun -deffnm npt0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
366
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
367 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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368 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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369 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
370 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
371 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
372 Reading file npt0.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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373 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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374
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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375
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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376 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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377 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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378
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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379 starting mdrun 'BioSimSpace System'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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380 50 steps, 0.1 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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381
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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382 Writing final coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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383
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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384 Core t (s) Wall t (s) (%)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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385 Time: 1.261 0.315 399.9
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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386 (ns/day) (hour/ns)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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387 Performance: 13.979 1.717
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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388
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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389 GROMACS reminds you: "I Was Born to Have Adventure" (F. Zappa)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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390
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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391 Constant pressure equilibration complete.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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392 Starting production MD simulation...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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393 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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394
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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395 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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396 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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397 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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398 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
399 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
400 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
401 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
402 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
403 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
404 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
405 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
406 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
407 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
408 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
409
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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410 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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411 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
412 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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413 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
414 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
415
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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416 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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417 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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418 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
419 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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420
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
421 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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422 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
423 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
424 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
425 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
426 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp -c ../NPT/npt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt0.cpt -o md0.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
427
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
428
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
429 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
430 With PME there is a minor soft core effect present at the cut-off,
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
431 proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
432 energy conservation, but usually other effects dominate. With a common
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
433 sigma value of 0.34 nm the fraction of the particle-particle potential at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
434 the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
435
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
436 Setting the LD random seed to -1773803540
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
437 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
438 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
439 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
440 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
441 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
442 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
443 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
444 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
445
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
446 NOTE 2 [file morph.top, line 232]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
447 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
448 an estimated oscillational period of 8.0e-03 ps, which is less than 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
449 times the time step of 1.0e-03 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
450 Maybe you forgot to change the constraints mdp option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
451
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
452 Number of degrees of freedom in T-Coupling group System is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
453 Reading Coordinates, Velocities and Box size from old trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
454 Will read whole trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
455 Last frame -1 time 0.050
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
456 Using frame at t = 0.05 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
457 Starting time for run is 0 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
458 Estimate for the relative computational load of the PME mesh part: 0.47
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
459
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
460 There were 2 notes
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
461
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
462 GROMACS reminds you: "God is a DJ" (Faithless)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
463
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
464 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
465 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
466 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
467 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
468 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
469 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
470 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
471 Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
472 Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
473 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
474 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
475 Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
476 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
477 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
478
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
479 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
480 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
481 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
482 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
483 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
484 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
485 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
486 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
487 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
488 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
489 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
490 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
491 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
492 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
493
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
494 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
495 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
496 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
497 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
498 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
499
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
500 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
501 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
502 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
503 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
504
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
505 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
506 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
507 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
508 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
509 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
510 gmx mdrun -deffnm md0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
511
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
512 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
513 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
514 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
515 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
516 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
517 Reading file md0.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
518 Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
519
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
520
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
521 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
522 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
523
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
524 starting mdrun 'BioSimSpace System'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
525 2000 steps, 2.0 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
526
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
527 Writing final coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
528
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
529 Core t (s) Wall t (s) (%)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
530 Time: 27.033 6.758 400.0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
531 (ns/day) (hour/ns)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
532 Performance: 25.581 0.938
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
533
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
534 GROMACS reminds you: "Don't You Wish You Never Met Her, Dirty Blue Gene?" (Captain Beefheart)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
535
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
536 Production MD complete.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
537 Ending. Job completed for lambda = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
538 Starting minimization for lambda = 1...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
539 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
540
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
541 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
542 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
543 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
544 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
545 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
546 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
547 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
548 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
549 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
550 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
551 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
552 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
553 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
554 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
555
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
556 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
557 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
558 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
559 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
560 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
561
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
562 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
563 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
564 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
565 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
566
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
567 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
568 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
569 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
570 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
571 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
572 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_1.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min1.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
573
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
574 Setting the LD random seed to -1393309481
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
575 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
576 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
577 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
578 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
579 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
580 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
581 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
582 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
583 Number of degrees of freedom in T-Coupling group rest is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
584 Estimate for the relative computational load of the PME mesh part: 0.21
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
585
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
586 GROMACS reminds you: "Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia." (Roald Hoffmann)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
587
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
588 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
589 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
590 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
591 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
592 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
593 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
594 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
595 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
596 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
597 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
598
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
599 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
600 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
601 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
602 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
603 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
604 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
605 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
606 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
607 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
608 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
609 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
610 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
611 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
612 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
613
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
614 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
615 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
616 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
617 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
618 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
619
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
620 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
621 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
622 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
623 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
624
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
625 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
626 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
627 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
628 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
629 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
630 gmx mdrun -deffnm min1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
631
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
632 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
633 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
634 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
635 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
636 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
637 Reading file min1.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
638
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
639 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
640 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
641
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
642
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
643 Steepest Descents:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
644 Tolerance (Fmax) = 1.00000e+02
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
645 Number of steps = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
646
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
647 Energy minimization reached the maximum number of steps before the forces
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
648 reached the requested precision Fmax < 100.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
649
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
650 writing lowest energy coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
651
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
652 Steepest Descents did not converge to Fmax < 100 in 11 steps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
653 Potential Energy = -8.3125391e+04
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
654 Maximum force = 2.1372287e+04 on atom 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
655 Norm of force = 5.1859150e+02
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
656
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
657 GROMACS reminds you: "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie" (Lola rennt)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
658
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
659 Starting constant volume equilibration...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
660 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
661
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
662 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
663 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
664 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
665 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
666 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
667 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
668 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
669 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
670 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
671 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
672 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
673 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
674 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
675 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
676
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
677 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
678 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
679 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
680 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
681 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
682
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
683 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
684 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
685 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
686 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
687
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
688 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
689 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
690 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
691 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
692 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
693 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_1.mdp -c ../EM/min1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt1.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
694
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
695 Setting the LD random seed to -1631510067
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
696 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
697 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
698 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
699 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
700 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
701 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
702 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
703 Velocities were taken from a Maxwell distribution at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
704 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
705
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
706 NOTE 1 [file morph.top, line 232]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
707 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
708 an estimated oscillational period of 8.0e-03 ps, which is less than 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
709 times the time step of 1.0e-03 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
710 Maybe you forgot to change the constraints mdp option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
711
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
712 Number of degrees of freedom in T-Coupling group System is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
713 Estimate for the relative computational load of the PME mesh part: 0.23
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
714
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
715 There was 1 note
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
716
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
717 GROMACS reminds you: "No great discovery was ever made without a bold guess." (Marie Curie)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
718
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
719 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
720 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
721 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
722 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
723 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
724 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
725 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
726 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
727 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
728 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
729 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
730 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
731 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
732 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
733
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
734 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
735 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
736 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
737 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
738 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
739 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
740 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
741 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
742 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
743 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
744 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
745 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
746 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
747 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
748
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
749 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
750 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
751 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
752 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
753 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
754
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
755 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
756 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
757 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
758 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
759
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
760 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
761 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
762 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
763 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
764 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
765 gmx mdrun -deffnm nvt1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
766
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
767 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
768 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
769 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
770 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
771 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
772 Reading file nvt1.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
773 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
774
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
775
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
776 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
777 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
778
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
779 starting mdrun 'BioSimSpace System'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
780 50 steps, 0.1 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
781
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
782 Writing final coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
783
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
784 Core t (s) Wall t (s) (%)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
785 Time: 1.273 0.318 399.9
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
786 (ns/day) (hour/ns)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
787 Performance: 13.842 1.734
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
788
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
789 GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
790
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
791 Constant volume equilibration complete.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
792 Starting constant pressure equilibration...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
793 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
794
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
795 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
796 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
797 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
798 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
799 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
800 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
801 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
802 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
803 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
804 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
805 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
806 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
807 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
808 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
809
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
810 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
811 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
812 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
813 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
814 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
815
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
816 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
817 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
818 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
819 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
820
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
821 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
822 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
823 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
824 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
825 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
826 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_1.mdp -c ../NVT/nvt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt1.cpt -o npt1.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
827
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
828 Setting the LD random seed to -166230178
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
829 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
830 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
831 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
832 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
833 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
834 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
835 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
836 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
837
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
838 NOTE 1 [file morph.top, line 232]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
839 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
840 an estimated oscillational period of 8.0e-03 ps, which is less than 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
841 times the time step of 1.0e-03 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
842 Maybe you forgot to change the constraints mdp option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
843
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
844 Number of degrees of freedom in T-Coupling group System is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
845 Reading Coordinates, Velocities and Box size from old trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
846 Will read whole trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
847 Last frame -1 time 0.050
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
848 Using frame at t = 0.05 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
849 Starting time for run is 0 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
850 Estimate for the relative computational load of the PME mesh part: 0.23
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
851
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
852 There was 1 note
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
853
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
854 GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
855
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
856 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
857 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
858 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
859 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
860 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
861 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
862 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
863 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
864 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
865 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
866 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
867 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
868 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
869 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
870
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
871 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
872 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
873 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
874 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
875 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
876 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
877 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
878 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
879 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
880 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
881 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
882 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
883 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
884 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
885
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
886 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
887 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
888 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
889 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
890 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
891
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
892 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
893 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
894 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
895 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
896
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
897 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
898 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
899 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
900 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
901 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
902 gmx mdrun -deffnm npt1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
903
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
904 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
905 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
906 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
907 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
908 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
909 Reading file npt1.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
910 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
911
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
912
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
913 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
914 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
915
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
916 starting mdrun 'BioSimSpace System'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
917 50 steps, 0.1 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
918
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
919 Writing final coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
920
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
921 Core t (s) Wall t (s) (%)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
922 Time: 1.310 0.328 399.9
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
923 (ns/day) (hour/ns)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
924 Performance: 13.448 1.785
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
925
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
926 GROMACS reminds you: "Don't Follow Me Home" (Throwing Muses)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
927
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
928 Constant pressure equilibration complete.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
929 Starting production MD simulation...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
930 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
931
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
932 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
933 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
934 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
935 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
936 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
937 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
938 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
939 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
940 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
941 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
942 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
943 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
944 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
945 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
946
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
947 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
948 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
949 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
950 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
951 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
952
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
953 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
954 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
955 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
956 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
957
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
958 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
959 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
960 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
961 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
962 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
963 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp -c ../NPT/npt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt1.cpt -o md1.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
964
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
965
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
966 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
967 With PME there is a minor soft core effect present at the cut-off,
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
968 proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
969 energy conservation, but usually other effects dominate. With a common
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
970 sigma value of 0.34 nm the fraction of the particle-particle potential at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
971 the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
972
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
973 Setting the LD random seed to -651728442
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
974 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
975 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
976 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
977 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
978 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
979 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
980 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
981 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
982
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
983 NOTE 2 [file morph.top, line 232]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
984 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
985 an estimated oscillational period of 8.0e-03 ps, which is less than 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
986 times the time step of 1.0e-03 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
987 Maybe you forgot to change the constraints mdp option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
988
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
989 Number of degrees of freedom in T-Coupling group System is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
990 Reading Coordinates, Velocities and Box size from old trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
991 Will read whole trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
992 Last frame -1 time 0.050
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
993 Using frame at t = 0.05 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
994 Starting time for run is 0 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
995 Estimate for the relative computational load of the PME mesh part: 0.47
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
996
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
997 There were 2 notes
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
998
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
999 GROMACS reminds you: "Beat On the Brat With a Baseball Bat" (The Ramones)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1000
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1001 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1002 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
1003 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
1004 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1005 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
1006 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1007 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1008 Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1009 Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
1010 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1011 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1012 Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1013 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1014 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1015
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1016 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1017 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1018 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1019 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1020 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1021 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1022 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1023 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1024 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1025 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1026 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1027 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1028 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1029 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1030
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1031 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1032 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1033 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1034 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1035 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1036
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1037 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1038 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1039 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1040 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1041
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1042 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1043 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1044 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1045 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1046 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1047 gmx mdrun -deffnm md1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1048
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1049 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1050 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1051 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1052 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1053 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1054 Reading file md1.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1055 Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1056
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1057
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1058 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1059 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1060
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1061 starting mdrun 'BioSimSpace System'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1062 2000 steps, 2.0 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1063
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1064 Writing final coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1065
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1066 Core t (s) Wall t (s) (%)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1067 Time: 27.548 6.887 400.0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1068 (ns/day) (hour/ns)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1069 Performance: 25.103 0.956
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1070
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1071 GROMACS reminds you: "Nothing is more anarchic than power." (Pier Paolo Pasolini)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1072
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1073 Production MD complete.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1074 Ending. Job completed for lambda = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1075 Starting minimization for lambda = 2...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1076 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1077
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1078 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1079 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1080 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1081 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1082 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1083 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1084 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1085 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1086 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1087 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1088 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1089 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1090 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1091 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1092
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1093 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1094 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1095 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1096 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1097 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1098
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1099 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1100 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1101 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1102 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1103
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1104 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1105 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1106 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1107 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1108 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1109 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_2.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min2.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1110
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1111 Setting the LD random seed to 886887101
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1112 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1113 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1114 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1115 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1116 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1117 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1118 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1119 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1120 Number of degrees of freedom in T-Coupling group rest is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1121 Estimate for the relative computational load of the PME mesh part: 0.21
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1122
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1123 GROMACS reminds you: "Sisters Have Always Fascinated Me" (Speech)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1124
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1125 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1126 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1127 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1128 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1129 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1130 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1131 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1132 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1133 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1134 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1135
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1136 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1137 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1138 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1139 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1140 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1141 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1142 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1143 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1144 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1145 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1146 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1147 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1148 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1149 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1150
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1151 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1152 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1153 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1154 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1155 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1156
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1157 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1158 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1159 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1160 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1161
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1162 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1163 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1164 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1165 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1166 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1167 gmx mdrun -deffnm min2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1168
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1169 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1170 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1171 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1172 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1173 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1174 Reading file min2.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1175
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1176 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1177 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1178
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1179
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1180 Steepest Descents:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1181 Tolerance (Fmax) = 1.00000e+02
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1182 Number of steps = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1183
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1184 Energy minimization reached the maximum number of steps before the forces
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1185 reached the requested precision Fmax < 100.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1186
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1187 writing lowest energy coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1188
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1189 Steepest Descents did not converge to Fmax < 100 in 11 steps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1190 Potential Energy = -8.3125391e+04
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1191 Maximum force = 2.1372287e+04 on atom 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1192 Norm of force = 5.1859150e+02
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1193
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1194 GROMACS reminds you: "The Candlelight Was Just Right" (Beastie Boys)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1195
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1196 Starting constant volume equilibration...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1197 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1198
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1199 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1200 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1201 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1202 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1203 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1204 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1205 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1206 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1207 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1208 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1209 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1210 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1211 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1212 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1213
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1214 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1215 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1216 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1217 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1218 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1219
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1220 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1221 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1222 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1223 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1224
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1225 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1226 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1227 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1228 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1229 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1230 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_2.mdp -c ../EM/min2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt2.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1231
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1232 Setting the LD random seed to -902054215
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1233 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1234 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1235 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1236 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1237 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1238 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1239 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1240 Velocities were taken from a Maxwell distribution at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1241 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1242
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1243 NOTE 1 [file morph.top, line 232]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1244 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1245 an estimated oscillational period of 8.0e-03 ps, which is less than 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1246 times the time step of 1.0e-03 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1247 Maybe you forgot to change the constraints mdp option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1248
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1249 Number of degrees of freedom in T-Coupling group System is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1250 Estimate for the relative computational load of the PME mesh part: 0.23
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1251
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1252 There was 1 note
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1253
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1254 GROMACS reminds you: "I spent a lot of money on booze, birds and fast cars. The rest I just squandered." (George Best)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1255
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1256 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1257 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1258 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1259 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1260 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1261 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1262 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1263 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1264 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1265 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1266 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1267 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1268 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1269 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1270
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1271 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1272 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1273 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1274 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1275 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1276 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1277 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1278 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1279 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1280 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1281 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1282 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1283 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1284 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1285
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1286 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1287 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1288 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1289 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1290 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1291
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1292 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1293 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1294 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1295 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1296
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1297 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1298 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1299 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1300 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1301 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1302 gmx mdrun -deffnm nvt2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1303
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1304 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1305 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1306 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1307 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1308 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1309 Reading file nvt2.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1310 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1311
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1312
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1313 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1314 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1315
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1316 starting mdrun 'BioSimSpace System'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1317 50 steps, 0.1 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1318
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1319 Writing final coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1320
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1321 Core t (s) Wall t (s) (%)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1322 Time: 1.308 0.327 399.9
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1323 (ns/day) (hour/ns)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1324 Performance: 13.471 1.782
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1325
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1326 GROMACS reminds you: "What if you're wrong about the great Ju Ju at the bottom of the sea?" (Richard Dawkins)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1327
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1328 Constant volume equilibration complete.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1329 Starting constant pressure equilibration...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1330 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1331
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1332 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1333 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1334 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1335 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1336 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1337 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1338 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1339 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1340 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1341 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1342 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1343 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1344 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1345 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1346
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1347 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1348 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1349 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1350 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1351 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1352
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1353 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1354 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1355 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1356 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1357
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1358 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1359 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1360 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1361 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1362 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1363 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_2.mdp -c ../NVT/nvt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt2.cpt -o npt2.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1364
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1365 Setting the LD random seed to -652502066
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1366 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1367 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1368 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1369 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1370 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1371 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1372 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1373 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1374
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1375 NOTE 1 [file morph.top, line 232]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1376 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1377 an estimated oscillational period of 8.0e-03 ps, which is less than 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1378 times the time step of 1.0e-03 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1379 Maybe you forgot to change the constraints mdp option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1380
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1381 Number of degrees of freedom in T-Coupling group System is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1382 Reading Coordinates, Velocities and Box size from old trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1383 Will read whole trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1384 Last frame -1 time 0.050
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1385 Using frame at t = 0.05 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1386 Starting time for run is 0 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1387 Estimate for the relative computational load of the PME mesh part: 0.23
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1388
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1389 There was 1 note
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1390
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1391 GROMACS reminds you: "When doing HPC, don't communica" (Jim Demmel)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1392
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1393 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1394 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1395 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1396 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1397 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1398 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1399 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1400 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1401 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1402 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1403 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1404 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1405 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1406 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1407
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1408 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1409 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1410 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1411 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1412 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1413 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1414 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1415 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1416 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1417 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1418 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1419 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1420 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1421 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1422
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1423 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1424 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1425 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1426 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1427 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1428
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1429 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1430 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1431 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1432 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1433
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1434 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1435 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1436 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1437 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1438 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1439 gmx mdrun -deffnm npt2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1440
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1441 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1442 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1443 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1444 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1445 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1446 Reading file npt2.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1447 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1448
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1449
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1450 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1451 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1452
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1453 starting mdrun 'BioSimSpace System'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1454 50 steps, 0.1 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1455
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1456 Writing final coordinates.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1457
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1458 Core t (s) Wall t (s) (%)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1459 Time: 1.290 0.323 399.9
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1460 (ns/day) (hour/ns)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1461 Performance: 13.659 1.757
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1462
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1463 GROMACS reminds you: "People are DNA's way of making more DNA." (Edward O. Wilson)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1464
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1465 Constant pressure equilibration complete.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1466 Starting production MD simulation...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1467 :-) GROMACS - gmx grompp, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1468
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1469 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1470 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1471 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1472 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1473 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1474 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1475 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1476 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1477 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1478 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1479 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1480 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1481 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1482 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1483
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1484 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1485 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1486 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1487 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1488 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1489
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1490 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1491 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1492 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1493 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1494
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1495 GROMACS: gmx grompp, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1496 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1497 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1498 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1499 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1500 gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp -c ../NPT/npt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt2.cpt -o md2.tpr
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1501
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1502
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1503 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1504 With PME there is a minor soft core effect present at the cut-off,
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1505 proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1506 energy conservation, but usually other effects dominate. With a common
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1507 sigma value of 0.34 nm the fraction of the particle-particle potential at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1508 the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1509
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1510 Setting the LD random seed to 551042888
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1511 Generated 45 of the 45 non-bonded parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1512 Generating 1-4 interactions: fudge = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1513 Generated 45 of the 45 1-4 parameter combinations
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1514 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1515 Excluding 3 bonded neighbours molecule type 'NA'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1516 Excluding 3 bonded neighbours molecule type 'CL'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1517 Excluding 3 bonded neighbours molecule type 'WAT'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1518 Removing all charge groups because cutoff-scheme=Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1519
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1520 NOTE 2 [file morph.top, line 232]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1521 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1522 an estimated oscillational period of 8.0e-03 ps, which is less than 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1523 times the time step of 1.0e-03 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1524 Maybe you forgot to change the constraints mdp option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1525
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1526 Number of degrees of freedom in T-Coupling group System is 12987.00
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1527 Reading Coordinates, Velocities and Box size from old trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1528 Will read whole trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1529 Last frame -1 time 0.050
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1530 Using frame at t = 0.05 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1531 Starting time for run is 0 ps
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1532 Estimate for the relative computational load of the PME mesh part: 0.47
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1533
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1534 There were 2 notes
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1535
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1536 GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1537
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1538 Analysing residue names:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1539 There are: 1 Other residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1540 There are: 10 Ion residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1541 There are: 2151 Water residues
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1542 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1543 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1544 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1545 Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1546 Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1547 Note that mdrun will redetermine rlist based on the actual pair-list setup
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1548 Calculating fourier grid dimensions for X Y Z
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1549 Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1550 This run will generate roughly 1 Mb of data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1551 :-) GROMACS - gmx mdrun, 2019.1 (-:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1552
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1553 GROMACS is written by:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1554 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1555 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1556 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1557 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1558 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1559 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1560 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1561 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1562 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1563 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1564 Christian Wennberg Maarten Wolf
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1565 and the project leaders:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1566 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1567
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1568 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1569 Copyright (c) 2001-2018, The GROMACS development team at
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1570 Uppsala University, Stockholm University and
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1571 the Royal Institute of Technology, Sweden.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1572 check out http://www.gromacs.org for more information.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1573
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1574 GROMACS is free software; you can redistribute it and/or modify it
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1575 under the terms of the GNU Lesser General Public License
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1576 as published by the Free Software Foundation; either version 2.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1577 of the License, or (at your option) any later version.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1578
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1579 GROMACS: gmx mdrun, version 2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1580 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1581 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1582 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1583 Command line:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1584 gmx mdrun -deffnm md2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1585
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1586 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1587 The current CPU can measure timings more accurately than the code in
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1588 gmx mdrun was configured to use. This might affect your simulation
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1589 speed as accurate timings are needed for load-balancing.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1590 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1591 Reading file md2.tpr, VERSION 2019.1 (single precision)
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1592 Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1593
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1594
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1595 Using 1 MPI thread
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1596 Using 4 OpenMP threads
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1597
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1598 starting mdrun 'BioSimSpace System'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1599 2000 steps, 2.0 ps.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1600
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1601 step 2: One or more water molecules can not be settled.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1602 Check for bad contacts and/or reduce the timestep if appropriate.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1603 Wrote pdb files with previous and current coordinates
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1604
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1605 WARNING: Listed nonbonded interaction between particles 6 and 15
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1606 at distance 47.750 which is larger than the table limit 1.860 nm.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1607
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1608 This is likely either a 1,4 interaction, or a listed interaction inside
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1609 a smaller molecule you are decoupling during a free energy calculation.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1610 Since interactions at distances beyond the table cannot be computed,
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1611 they are skipped until they are inside the table limit again. You will
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1612 only see this message once, even if it occurs for several interactions.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1613
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1614 IMPORTANT: This should not happen in a stable simulation, so there is
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1615 probably something wrong with your system. Only change the table-extension
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1616 distance in the mdp file if you are really sure that is the reason.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1617
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1618
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1619
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1620 WARNING: Listed nonbonded interaction between particles 2 and 15
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1621 at distance 47.627 which is larger than the table limit 1.860 nm.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1622
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1623 This is likely either a 1,4 interaction, or a listed interaction inside
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1624 a smaller molecule you are decoupling during a free energy calculation.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1625 Since interactions at distances beyond the table cannot be computed,
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1626 they are skipped until they are inside the table limit again. You will
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1627 only see this message once, even if it occurs for several interactions.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1628
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1629 IMPORTANT: This should not happen in a stable simulation, so there is
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1630 probably something wrong with your system. Only change the table-extension
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1631 distance in the mdp file if you are really sure that is the reason.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1632
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1633
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1634 /scratch2/tsenapathi/Projects/BRIDGE/galaxy-tools-compchem/tools/free_energy/alchemical_run/gmx_fep.sh: line 104: 13890 Segmentation fault gmx mdrun -deffnm md$LAMBDA
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1635 Production MD complete.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1636 Ending. Job completed for lambda = 2