Mercurial > repos > chemteam > gmx_fep
view alchemical_run/test-data/Report.txt @ 0:19d1d4c30402 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
| author | chemteam |
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| date | Mon, 11 Nov 2019 13:20:39 -0500 |
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Starting minimization for lambda = 0... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM Command line: 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 Setting the LD random seed to -127141127 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 12987.00 Estimate for the relative computational load of the PME mesh part: 0.21 GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM Command line: gmx mdrun -deffnm min0 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file min0.tpr, VERSION 2019.1 (single precision) Using 1 MPI thread Using 4 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+02 Number of steps = 10 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 100. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 100 in 11 steps. Potential Energy = -8.3125391e+04 Maximum force = 2.1372287e+04 on atom 1 Norm of force = 5.1859150e+02 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) Starting constant volume equilibration... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT Command line: 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 Setting the LD random seed to -187712966 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet NOTE 1 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Estimate for the relative computational load of the PME mesh part: 0.23 There was 1 note GROMACS reminds you: "Nada e organico, e tudo programado" (Pitty) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT Command line: gmx mdrun -deffnm nvt0 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file nvt0.tpr, VERSION 2019.1 (single precision) Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 50 steps, 0.1 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.458 0.365 399.9 (ns/day) (hour/ns) Performance: 12.084 1.986 GROMACS reminds you: "I Quit My Job Blowing Leaves" (Beck) Constant volume equilibration complete. Starting constant pressure equilibration... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT Command line: 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 Setting the LD random seed to 2038796930 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet NOTE 1 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 0.050 Using frame at t = 0.05 ps Starting time for run is 0 ps Estimate for the relative computational load of the PME mesh part: 0.23 There was 1 note GROMACS reminds you: "Act like Prometheus would" (Gogol Bordello) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT Command line: gmx mdrun -deffnm npt0 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file npt0.tpr, VERSION 2019.1 (single precision) Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 50 steps, 0.1 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.261 0.315 399.9 (ns/day) (hour/ns) Performance: 13.979 1.717 GROMACS reminds you: "I Was Born to Have Adventure" (F. Zappa) Constant pressure equilibration complete. Starting production MD simulation... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD Command line: 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 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. Setting the LD random seed to -1773803540 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet NOTE 2 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 0.050 Using frame at t = 0.05 ps Starting time for run is 0 ps Estimate for the relative computational load of the PME mesh part: 0.47 There were 2 notes GROMACS reminds you: "God is a DJ" (Faithless) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD Command line: gmx mdrun -deffnm md0 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file md0.tpr, VERSION 2019.1 (single precision) Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 2000 steps, 2.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 27.033 6.758 400.0 (ns/day) (hour/ns) Performance: 25.581 0.938 GROMACS reminds you: "Don't You Wish You Never Met Her, Dirty Blue Gene?" (Captain Beefheart) Production MD complete. Ending. Job completed for lambda = 0 Starting minimization for lambda = 1... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM Command line: 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 Setting the LD random seed to -1393309481 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 12987.00 Estimate for the relative computational load of the PME mesh part: 0.21 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) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM Command line: gmx mdrun -deffnm min1 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file min1.tpr, VERSION 2019.1 (single precision) Using 1 MPI thread Using 4 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+02 Number of steps = 10 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 100. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 100 in 11 steps. Potential Energy = -8.3125391e+04 Maximum force = 2.1372287e+04 on atom 1 Norm of force = 5.1859150e+02 GROMACS reminds you: "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie" (Lola rennt) Starting constant volume equilibration... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT Command line: 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 Setting the LD random seed to -1631510067 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet NOTE 1 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Estimate for the relative computational load of the PME mesh part: 0.23 There was 1 note GROMACS reminds you: "No great discovery was ever made without a bold guess." (Marie Curie) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT Command line: gmx mdrun -deffnm nvt1 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file nvt1.tpr, VERSION 2019.1 (single precision) Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 50 steps, 0.1 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.273 0.318 399.9 (ns/day) (hour/ns) Performance: 13.842 1.734 GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter) Constant volume equilibration complete. Starting constant pressure equilibration... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT Command line: 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 Setting the LD random seed to -166230178 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet NOTE 1 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 0.050 Using frame at t = 0.05 ps Starting time for run is 0 ps Estimate for the relative computational load of the PME mesh part: 0.23 There was 1 note GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT Command line: gmx mdrun -deffnm npt1 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file npt1.tpr, VERSION 2019.1 (single precision) Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 50 steps, 0.1 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.310 0.328 399.9 (ns/day) (hour/ns) Performance: 13.448 1.785 GROMACS reminds you: "Don't Follow Me Home" (Throwing Muses) Constant pressure equilibration complete. Starting production MD simulation... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD Command line: 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 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. Setting the LD random seed to -651728442 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet NOTE 2 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 0.050 Using frame at t = 0.05 ps Starting time for run is 0 ps Estimate for the relative computational load of the PME mesh part: 0.47 There were 2 notes GROMACS reminds you: "Beat On the Brat With a Baseball Bat" (The Ramones) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD Command line: gmx mdrun -deffnm md1 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file md1.tpr, VERSION 2019.1 (single precision) Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 2000 steps, 2.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 27.548 6.887 400.0 (ns/day) (hour/ns) Performance: 25.103 0.956 GROMACS reminds you: "Nothing is more anarchic than power." (Pier Paolo Pasolini) Production MD complete. Ending. Job completed for lambda = 1 Starting minimization for lambda = 2... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM Command line: 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 Setting the LD random seed to 886887101 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 12987.00 Estimate for the relative computational load of the PME mesh part: 0.21 GROMACS reminds you: "Sisters Have Always Fascinated Me" (Speech) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM Command line: gmx mdrun -deffnm min2 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file min2.tpr, VERSION 2019.1 (single precision) Using 1 MPI thread Using 4 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+02 Number of steps = 10 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 100. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 100 in 11 steps. Potential Energy = -8.3125391e+04 Maximum force = 2.1372287e+04 on atom 1 Norm of force = 5.1859150e+02 GROMACS reminds you: "The Candlelight Was Just Right" (Beastie Boys) Starting constant volume equilibration... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT Command line: 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 Setting the LD random seed to -902054215 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet NOTE 1 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Estimate for the relative computational load of the PME mesh part: 0.23 There was 1 note GROMACS reminds you: "I spent a lot of money on booze, birds and fast cars. The rest I just squandered." (George Best) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT Command line: gmx mdrun -deffnm nvt2 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file nvt2.tpr, VERSION 2019.1 (single precision) Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 50 steps, 0.1 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.308 0.327 399.9 (ns/day) (hour/ns) Performance: 13.471 1.782 GROMACS reminds you: "What if you're wrong about the great Ju Ju at the bottom of the sea?" (Richard Dawkins) Constant volume equilibration complete. Starting constant pressure equilibration... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT Command line: 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 Setting the LD random seed to -652502066 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet NOTE 1 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 0.050 Using frame at t = 0.05 ps Starting time for run is 0 ps Estimate for the relative computational load of the PME mesh part: 0.23 There was 1 note GROMACS reminds you: "When doing HPC, don't communica" (Jim Demmel) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT Command line: gmx mdrun -deffnm npt2 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file npt2.tpr, VERSION 2019.1 (single precision) Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 50 steps, 0.1 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.290 0.323 399.9 (ns/day) (hour/ns) Performance: 13.659 1.757 GROMACS reminds you: "People are DNA's way of making more DNA." (Edward O. Wilson) Constant pressure equilibration complete. Starting production MD simulation... :-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD Command line: 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 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. Setting the LD random seed to 551042888 Generated 45 of the 45 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 45 of the 45 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Merged_Molecule' Excluding 3 bonded neighbours molecule type 'NA' Excluding 3 bonded neighbours molecule type 'CL' Excluding 3 bonded neighbours molecule type 'WAT' Removing all charge groups because cutoff-scheme=Verlet NOTE 2 [file morph.top, line 232]: The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has an estimated oscillational period of 8.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 12987.00 Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 0.050 Using frame at t = 0.05 ps Starting time for run is 0 ps Estimate for the relative computational load of the PME mesh part: 0.47 There were 2 notes GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess) Analysing residue names: There are: 1 Other residues There are: 10 Ion residues There are: 2151 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 This run will generate roughly 1 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019.1 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD Command line: gmx mdrun -deffnm md2 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file md2.tpr, VERSION 2019.1 (single precision) Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 Using 1 MPI thread Using 4 OpenMP threads starting mdrun 'BioSimSpace System' 2000 steps, 2.0 ps. step 2: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates WARNING: Listed nonbonded interaction between particles 6 and 15 at distance 47.750 which is larger than the table limit 1.860 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. WARNING: Listed nonbonded interaction between particles 2 and 15 at distance 47.627 which is larger than the table limit 1.860 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. /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 Production MD complete. Ending. Job completed for lambda = 2