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comparison 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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1 Starting minimization for lambda = 0...
2 :-) GROMACS - gmx grompp, 2019.1 (-:
3
4 GROMACS is written by:
5 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
6 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
7 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
8 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
9 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
10 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
11 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
12 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
13 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
14 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
15 Christian Wennberg Maarten Wolf
16 and the project leaders:
17 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
18
19 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
20 Copyright (c) 2001-2018, The GROMACS development team at
21 Uppsala University, Stockholm University and
22 the Royal Institute of Technology, Sweden.
23 check out http://www.gromacs.org for more information.
24
25 GROMACS is free software; you can redistribute it and/or modify it
26 under the terms of the GNU Lesser General Public License
27 as published by the Free Software Foundation; either version 2.1
28 of the License, or (at your option) any later version.
29
30 GROMACS: gmx grompp, version 2019.1
31 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
32 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
33 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM
34 Command line:
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
36
37 Setting the LD random seed to -127141127
38 Generated 45 of the 45 non-bonded parameter combinations
39 Generating 1-4 interactions: fudge = 0.5
40 Generated 45 of the 45 1-4 parameter combinations
41 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
42 Excluding 3 bonded neighbours molecule type 'NA'
43 Excluding 3 bonded neighbours molecule type 'CL'
44 Excluding 3 bonded neighbours molecule type 'WAT'
45 Removing all charge groups because cutoff-scheme=Verlet
46 Number of degrees of freedom in T-Coupling group rest is 12987.00
47 Estimate for the relative computational load of the PME mesh part: 0.21
48
49 GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)
50
51 Analysing residue names:
52 There are: 1 Other residues
53 There are: 10 Ion residues
54 There are: 2151 Water residues
55 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
56 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
57 Calculating fourier grid dimensions for X Y Z
58 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
59 This run will generate roughly 1 Mb of data
60 :-) GROMACS - gmx mdrun, 2019.1 (-:
61
62 GROMACS is written by:
63 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
64 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
65 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
66 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
67 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
68 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
69 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
70 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
71 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
72 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
73 Christian Wennberg Maarten Wolf
74 and the project leaders:
75 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
76
77 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
78 Copyright (c) 2001-2018, The GROMACS development team at
79 Uppsala University, Stockholm University and
80 the Royal Institute of Technology, Sweden.
81 check out http://www.gromacs.org for more information.
82
83 GROMACS is free software; you can redistribute it and/or modify it
84 under the terms of the GNU Lesser General Public License
85 as published by the Free Software Foundation; either version 2.1
86 of the License, or (at your option) any later version.
87
88 GROMACS: gmx mdrun, version 2019.1
89 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
90 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
91 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM
92 Command line:
93 gmx mdrun -deffnm min0
94
95 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
96 The current CPU can measure timings more accurately than the code in
97 gmx mdrun was configured to use. This might affect your simulation
98 speed as accurate timings are needed for load-balancing.
99 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
100 Reading file min0.tpr, VERSION 2019.1 (single precision)
101
102 Using 1 MPI thread
103 Using 4 OpenMP threads
104
105
106 Steepest Descents:
107 Tolerance (Fmax) = 1.00000e+02
108 Number of steps = 10
109
110 Energy minimization reached the maximum number of steps before the forces
111 reached the requested precision Fmax < 100.
112
113 writing lowest energy coordinates.
114
115 Steepest Descents did not converge to Fmax < 100 in 11 steps.
116 Potential Energy = -8.3125391e+04
117 Maximum force = 2.1372287e+04 on atom 1
118 Norm of force = 5.1859150e+02
119
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)
121
122 Starting constant volume equilibration...
123 :-) GROMACS - gmx grompp, 2019.1 (-:
124
125 GROMACS is written by:
126 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
127 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
128 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
129 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
130 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
131 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
132 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
133 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
134 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
135 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
136 Christian Wennberg Maarten Wolf
137 and the project leaders:
138 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
139
140 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
141 Copyright (c) 2001-2018, The GROMACS development team at
142 Uppsala University, Stockholm University and
143 the Royal Institute of Technology, Sweden.
144 check out http://www.gromacs.org for more information.
145
146 GROMACS is free software; you can redistribute it and/or modify it
147 under the terms of the GNU Lesser General Public License
148 as published by the Free Software Foundation; either version 2.1
149 of the License, or (at your option) any later version.
150
151 GROMACS: gmx grompp, version 2019.1
152 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
153 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
154 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT
155 Command line:
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
157
158 Setting the LD random seed to -187712966
159 Generated 45 of the 45 non-bonded parameter combinations
160 Generating 1-4 interactions: fudge = 0.5
161 Generated 45 of the 45 1-4 parameter combinations
162 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
163 Excluding 3 bonded neighbours molecule type 'NA'
164 Excluding 3 bonded neighbours molecule type 'CL'
165 Excluding 3 bonded neighbours molecule type 'WAT'
166 Velocities were taken from a Maxwell distribution at 300 K
167 Removing all charge groups because cutoff-scheme=Verlet
168
169 NOTE 1 [file morph.top, line 232]:
170 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
171 an estimated oscillational period of 8.0e-03 ps, which is less than 10
172 times the time step of 1.0e-03 ps.
173 Maybe you forgot to change the constraints mdp option.
174
175 Number of degrees of freedom in T-Coupling group System is 12987.00
176 Estimate for the relative computational load of the PME mesh part: 0.23
177
178 There was 1 note
179
180 GROMACS reminds you: "Nada e organico, e tudo programado" (Pitty)
181
182 Analysing residue names:
183 There are: 1 Other residues
184 There are: 10 Ion residues
185 There are: 2151 Water residues
186 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
187 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
188 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
189 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
190 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
191 Note that mdrun will redetermine rlist based on the actual pair-list setup
192 Calculating fourier grid dimensions for X Y Z
193 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
194 This run will generate roughly 1 Mb of data
195 :-) GROMACS - gmx mdrun, 2019.1 (-:
196
197 GROMACS is written by:
198 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
199 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
200 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
201 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
202 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
203 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
204 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
205 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
206 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
207 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
208 Christian Wennberg Maarten Wolf
209 and the project leaders:
210 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
211
212 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
213 Copyright (c) 2001-2018, The GROMACS development team at
214 Uppsala University, Stockholm University and
215 the Royal Institute of Technology, Sweden.
216 check out http://www.gromacs.org for more information.
217
218 GROMACS is free software; you can redistribute it and/or modify it
219 under the terms of the GNU Lesser General Public License
220 as published by the Free Software Foundation; either version 2.1
221 of the License, or (at your option) any later version.
222
223 GROMACS: gmx mdrun, version 2019.1
224 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
225 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
226 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT
227 Command line:
228 gmx mdrun -deffnm nvt0
229
230 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
231 The current CPU can measure timings more accurately than the code in
232 gmx mdrun was configured to use. This might affect your simulation
233 speed as accurate timings are needed for load-balancing.
234 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
235 Reading file nvt0.tpr, VERSION 2019.1 (single precision)
236 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
237
238
239 Using 1 MPI thread
240 Using 4 OpenMP threads
241
242 starting mdrun 'BioSimSpace System'
243 50 steps, 0.1 ps.
244
245 Writing final coordinates.
246
247 Core t (s) Wall t (s) (%)
248 Time: 1.458 0.365 399.9
249 (ns/day) (hour/ns)
250 Performance: 12.084 1.986
251
252 GROMACS reminds you: "I Quit My Job Blowing Leaves" (Beck)
253
254 Constant volume equilibration complete.
255 Starting constant pressure equilibration...
256 :-) GROMACS - gmx grompp, 2019.1 (-:
257
258 GROMACS is written by:
259 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
260 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
261 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
262 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
263 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
264 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
265 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
266 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
267 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
268 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
269 Christian Wennberg Maarten Wolf
270 and the project leaders:
271 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
272
273 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
274 Copyright (c) 2001-2018, The GROMACS development team at
275 Uppsala University, Stockholm University and
276 the Royal Institute of Technology, Sweden.
277 check out http://www.gromacs.org for more information.
278
279 GROMACS is free software; you can redistribute it and/or modify it
280 under the terms of the GNU Lesser General Public License
281 as published by the Free Software Foundation; either version 2.1
282 of the License, or (at your option) any later version.
283
284 GROMACS: gmx grompp, version 2019.1
285 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
286 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
287 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT
288 Command line:
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
290
291 Setting the LD random seed to 2038796930
292 Generated 45 of the 45 non-bonded parameter combinations
293 Generating 1-4 interactions: fudge = 0.5
294 Generated 45 of the 45 1-4 parameter combinations
295 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
296 Excluding 3 bonded neighbours molecule type 'NA'
297 Excluding 3 bonded neighbours molecule type 'CL'
298 Excluding 3 bonded neighbours molecule type 'WAT'
299 Removing all charge groups because cutoff-scheme=Verlet
300
301 NOTE 1 [file morph.top, line 232]:
302 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
303 an estimated oscillational period of 8.0e-03 ps, which is less than 10
304 times the time step of 1.0e-03 ps.
305 Maybe you forgot to change the constraints mdp option.
306
307 Number of degrees of freedom in T-Coupling group System is 12987.00
308 Reading Coordinates, Velocities and Box size from old trajectory
309 Will read whole trajectory
310
311 Last frame -1 time 0.050
312 Using frame at t = 0.05 ps
313 Starting time for run is 0 ps
314 Estimate for the relative computational load of the PME mesh part: 0.23
315
316 There was 1 note
317
318 GROMACS reminds you: "Act like Prometheus would" (Gogol Bordello)
319
320 Analysing residue names:
321 There are: 1 Other residues
322 There are: 10 Ion residues
323 There are: 2151 Water residues
324 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
325 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
326 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
327 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
328 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
329 Note that mdrun will redetermine rlist based on the actual pair-list setup
330 Calculating fourier grid dimensions for X Y Z
331 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
332 This run will generate roughly 1 Mb of data
333 :-) GROMACS - gmx mdrun, 2019.1 (-:
334
335 GROMACS is written by:
336 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
337 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
338 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
339 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
340 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
341 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
342 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
343 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
344 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
345 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
346 Christian Wennberg Maarten Wolf
347 and the project leaders:
348 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
349
350 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
351 Copyright (c) 2001-2018, The GROMACS development team at
352 Uppsala University, Stockholm University and
353 the Royal Institute of Technology, Sweden.
354 check out http://www.gromacs.org for more information.
355
356 GROMACS is free software; you can redistribute it and/or modify it
357 under the terms of the GNU Lesser General Public License
358 as published by the Free Software Foundation; either version 2.1
359 of the License, or (at your option) any later version.
360
361 GROMACS: gmx mdrun, version 2019.1
362 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
363 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
364 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT
365 Command line:
366 gmx mdrun -deffnm npt0
367
368 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
369 The current CPU can measure timings more accurately than the code in
370 gmx mdrun was configured to use. This might affect your simulation
371 speed as accurate timings are needed for load-balancing.
372 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
373 Reading file npt0.tpr, VERSION 2019.1 (single precision)
374 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
375
376
377 Using 1 MPI thread
378 Using 4 OpenMP threads
379
380 starting mdrun 'BioSimSpace System'
381 50 steps, 0.1 ps.
382
383 Writing final coordinates.
384
385 Core t (s) Wall t (s) (%)
386 Time: 1.261 0.315 399.9
387 (ns/day) (hour/ns)
388 Performance: 13.979 1.717
389
390 GROMACS reminds you: "I Was Born to Have Adventure" (F. Zappa)
391
392 Constant pressure equilibration complete.
393 Starting production MD simulation...
394 :-) GROMACS - gmx grompp, 2019.1 (-:
395
396 GROMACS is written by:
397 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
398 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
399 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
400 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
401 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
402 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
403 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
404 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
405 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
406 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
407 Christian Wennberg Maarten Wolf
408 and the project leaders:
409 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
410
411 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
412 Copyright (c) 2001-2018, The GROMACS development team at
413 Uppsala University, Stockholm University and
414 the Royal Institute of Technology, Sweden.
415 check out http://www.gromacs.org for more information.
416
417 GROMACS is free software; you can redistribute it and/or modify it
418 under the terms of the GNU Lesser General Public License
419 as published by the Free Software Foundation; either version 2.1
420 of the License, or (at your option) any later version.
421
422 GROMACS: gmx grompp, version 2019.1
423 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
424 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
425 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD
426 Command line:
427 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
428
429
430 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp]:
431 With PME there is a minor soft core effect present at the cut-off,
432 proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
433 energy conservation, but usually other effects dominate. With a common
434 sigma value of 0.34 nm the fraction of the particle-particle potential at
435 the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
436
437 Setting the LD random seed to -1773803540
438 Generated 45 of the 45 non-bonded parameter combinations
439 Generating 1-4 interactions: fudge = 0.5
440 Generated 45 of the 45 1-4 parameter combinations
441 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
442 Excluding 3 bonded neighbours molecule type 'NA'
443 Excluding 3 bonded neighbours molecule type 'CL'
444 Excluding 3 bonded neighbours molecule type 'WAT'
445 Removing all charge groups because cutoff-scheme=Verlet
446
447 NOTE 2 [file morph.top, line 232]:
448 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
449 an estimated oscillational period of 8.0e-03 ps, which is less than 10
450 times the time step of 1.0e-03 ps.
451 Maybe you forgot to change the constraints mdp option.
452
453 Number of degrees of freedom in T-Coupling group System is 12987.00
454 Reading Coordinates, Velocities and Box size from old trajectory
455 Will read whole trajectory
456
457 Last frame -1 time 0.050
458 Using frame at t = 0.05 ps
459 Starting time for run is 0 ps
460 Estimate for the relative computational load of the PME mesh part: 0.47
461
462 There were 2 notes
463
464 GROMACS reminds you: "God is a DJ" (Faithless)
465
466 Analysing residue names:
467 There are: 1 Other residues
468 There are: 10 Ion residues
469 There are: 2151 Water residues
470 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
471 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
472 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
473 Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
474 Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
475 Note that mdrun will redetermine rlist based on the actual pair-list setup
476 Calculating fourier grid dimensions for X Y Z
477 Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
478 This run will generate roughly 1 Mb of data
479 :-) GROMACS - gmx mdrun, 2019.1 (-:
480
481 GROMACS is written by:
482 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
483 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
484 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
485 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
486 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
487 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
488 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
489 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
490 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
491 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
492 Christian Wennberg Maarten Wolf
493 and the project leaders:
494 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
495
496 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
497 Copyright (c) 2001-2018, The GROMACS development team at
498 Uppsala University, Stockholm University and
499 the Royal Institute of Technology, Sweden.
500 check out http://www.gromacs.org for more information.
501
502 GROMACS is free software; you can redistribute it and/or modify it
503 under the terms of the GNU Lesser General Public License
504 as published by the Free Software Foundation; either version 2.1
505 of the License, or (at your option) any later version.
506
507 GROMACS: gmx mdrun, version 2019.1
508 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
509 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
510 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD
511 Command line:
512 gmx mdrun -deffnm md0
513
514 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
515 The current CPU can measure timings more accurately than the code in
516 gmx mdrun was configured to use. This might affect your simulation
517 speed as accurate timings are needed for load-balancing.
518 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
519 Reading file md0.tpr, VERSION 2019.1 (single precision)
520 Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
521
522
523 Using 1 MPI thread
524 Using 4 OpenMP threads
525
526 starting mdrun 'BioSimSpace System'
527 2000 steps, 2.0 ps.
528
529 Writing final coordinates.
530
531 Core t (s) Wall t (s) (%)
532 Time: 27.033 6.758 400.0
533 (ns/day) (hour/ns)
534 Performance: 25.581 0.938
535
536 GROMACS reminds you: "Don't You Wish You Never Met Her, Dirty Blue Gene?" (Captain Beefheart)
537
538 Production MD complete.
539 Ending. Job completed for lambda = 0
540 Starting minimization for lambda = 1...
541 :-) GROMACS - gmx grompp, 2019.1 (-:
542
543 GROMACS is written by:
544 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
545 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
546 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
547 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
548 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
549 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
550 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
551 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
552 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
553 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
554 Christian Wennberg Maarten Wolf
555 and the project leaders:
556 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
557
558 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
559 Copyright (c) 2001-2018, The GROMACS development team at
560 Uppsala University, Stockholm University and
561 the Royal Institute of Technology, Sweden.
562 check out http://www.gromacs.org for more information.
563
564 GROMACS is free software; you can redistribute it and/or modify it
565 under the terms of the GNU Lesser General Public License
566 as published by the Free Software Foundation; either version 2.1
567 of the License, or (at your option) any later version.
568
569 GROMACS: gmx grompp, version 2019.1
570 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
571 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
572 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM
573 Command line:
574 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
575
576 Setting the LD random seed to -1393309481
577 Generated 45 of the 45 non-bonded parameter combinations
578 Generating 1-4 interactions: fudge = 0.5
579 Generated 45 of the 45 1-4 parameter combinations
580 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
581 Excluding 3 bonded neighbours molecule type 'NA'
582 Excluding 3 bonded neighbours molecule type 'CL'
583 Excluding 3 bonded neighbours molecule type 'WAT'
584 Removing all charge groups because cutoff-scheme=Verlet
585 Number of degrees of freedom in T-Coupling group rest is 12987.00
586 Estimate for the relative computational load of the PME mesh part: 0.21
587
588 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)
589
590 Analysing residue names:
591 There are: 1 Other residues
592 There are: 10 Ion residues
593 There are: 2151 Water residues
594 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
595 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
596 Calculating fourier grid dimensions for X Y Z
597 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
598 This run will generate roughly 1 Mb of data
599 :-) GROMACS - gmx mdrun, 2019.1 (-:
600
601 GROMACS is written by:
602 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
603 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
604 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
605 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
606 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
607 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
608 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
609 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
610 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
611 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
612 Christian Wennberg Maarten Wolf
613 and the project leaders:
614 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
615
616 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
617 Copyright (c) 2001-2018, The GROMACS development team at
618 Uppsala University, Stockholm University and
619 the Royal Institute of Technology, Sweden.
620 check out http://www.gromacs.org for more information.
621
622 GROMACS is free software; you can redistribute it and/or modify it
623 under the terms of the GNU Lesser General Public License
624 as published by the Free Software Foundation; either version 2.1
625 of the License, or (at your option) any later version.
626
627 GROMACS: gmx mdrun, version 2019.1
628 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
629 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
630 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM
631 Command line:
632 gmx mdrun -deffnm min1
633
634 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
635 The current CPU can measure timings more accurately than the code in
636 gmx mdrun was configured to use. This might affect your simulation
637 speed as accurate timings are needed for load-balancing.
638 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
639 Reading file min1.tpr, VERSION 2019.1 (single precision)
640
641 Using 1 MPI thread
642 Using 4 OpenMP threads
643
644
645 Steepest Descents:
646 Tolerance (Fmax) = 1.00000e+02
647 Number of steps = 10
648
649 Energy minimization reached the maximum number of steps before the forces
650 reached the requested precision Fmax < 100.
651
652 writing lowest energy coordinates.
653
654 Steepest Descents did not converge to Fmax < 100 in 11 steps.
655 Potential Energy = -8.3125391e+04
656 Maximum force = 2.1372287e+04 on atom 1
657 Norm of force = 5.1859150e+02
658
659 GROMACS reminds you: "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie" (Lola rennt)
660
661 Starting constant volume equilibration...
662 :-) GROMACS - gmx grompp, 2019.1 (-:
663
664 GROMACS is written by:
665 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
666 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
667 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
668 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
669 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
670 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
671 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
672 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
673 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
674 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
675 Christian Wennberg Maarten Wolf
676 and the project leaders:
677 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
678
679 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
680 Copyright (c) 2001-2018, The GROMACS development team at
681 Uppsala University, Stockholm University and
682 the Royal Institute of Technology, Sweden.
683 check out http://www.gromacs.org for more information.
684
685 GROMACS is free software; you can redistribute it and/or modify it
686 under the terms of the GNU Lesser General Public License
687 as published by the Free Software Foundation; either version 2.1
688 of the License, or (at your option) any later version.
689
690 GROMACS: gmx grompp, version 2019.1
691 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
692 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
693 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT
694 Command line:
695 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
696
697 Setting the LD random seed to -1631510067
698 Generated 45 of the 45 non-bonded parameter combinations
699 Generating 1-4 interactions: fudge = 0.5
700 Generated 45 of the 45 1-4 parameter combinations
701 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
702 Excluding 3 bonded neighbours molecule type 'NA'
703 Excluding 3 bonded neighbours molecule type 'CL'
704 Excluding 3 bonded neighbours molecule type 'WAT'
705 Velocities were taken from a Maxwell distribution at 300 K
706 Removing all charge groups because cutoff-scheme=Verlet
707
708 NOTE 1 [file morph.top, line 232]:
709 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
710 an estimated oscillational period of 8.0e-03 ps, which is less than 10
711 times the time step of 1.0e-03 ps.
712 Maybe you forgot to change the constraints mdp option.
713
714 Number of degrees of freedom in T-Coupling group System is 12987.00
715 Estimate for the relative computational load of the PME mesh part: 0.23
716
717 There was 1 note
718
719 GROMACS reminds you: "No great discovery was ever made without a bold guess." (Marie Curie)
720
721 Analysing residue names:
722 There are: 1 Other residues
723 There are: 10 Ion residues
724 There are: 2151 Water residues
725 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
726 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
727 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
728 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
729 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
730 Note that mdrun will redetermine rlist based on the actual pair-list setup
731 Calculating fourier grid dimensions for X Y Z
732 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
733 This run will generate roughly 1 Mb of data
734 :-) GROMACS - gmx mdrun, 2019.1 (-:
735
736 GROMACS is written by:
737 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
738 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
739 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
740 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
741 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
742 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
743 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
744 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
745 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
746 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
747 Christian Wennberg Maarten Wolf
748 and the project leaders:
749 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
750
751 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
752 Copyright (c) 2001-2018, The GROMACS development team at
753 Uppsala University, Stockholm University and
754 the Royal Institute of Technology, Sweden.
755 check out http://www.gromacs.org for more information.
756
757 GROMACS is free software; you can redistribute it and/or modify it
758 under the terms of the GNU Lesser General Public License
759 as published by the Free Software Foundation; either version 2.1
760 of the License, or (at your option) any later version.
761
762 GROMACS: gmx mdrun, version 2019.1
763 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
764 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
765 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT
766 Command line:
767 gmx mdrun -deffnm nvt1
768
769 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
770 The current CPU can measure timings more accurately than the code in
771 gmx mdrun was configured to use. This might affect your simulation
772 speed as accurate timings are needed for load-balancing.
773 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
774 Reading file nvt1.tpr, VERSION 2019.1 (single precision)
775 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
776
777
778 Using 1 MPI thread
779 Using 4 OpenMP threads
780
781 starting mdrun 'BioSimSpace System'
782 50 steps, 0.1 ps.
783
784 Writing final coordinates.
785
786 Core t (s) Wall t (s) (%)
787 Time: 1.273 0.318 399.9
788 (ns/day) (hour/ns)
789 Performance: 13.842 1.734
790
791 GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter)
792
793 Constant volume equilibration complete.
794 Starting constant pressure equilibration...
795 :-) GROMACS - gmx grompp, 2019.1 (-:
796
797 GROMACS is written by:
798 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
799 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
800 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
801 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
802 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
803 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
804 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
805 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
806 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
807 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
808 Christian Wennberg Maarten Wolf
809 and the project leaders:
810 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
811
812 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
813 Copyright (c) 2001-2018, The GROMACS development team at
814 Uppsala University, Stockholm University and
815 the Royal Institute of Technology, Sweden.
816 check out http://www.gromacs.org for more information.
817
818 GROMACS is free software; you can redistribute it and/or modify it
819 under the terms of the GNU Lesser General Public License
820 as published by the Free Software Foundation; either version 2.1
821 of the License, or (at your option) any later version.
822
823 GROMACS: gmx grompp, version 2019.1
824 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
825 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
826 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT
827 Command line:
828 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
829
830 Setting the LD random seed to -166230178
831 Generated 45 of the 45 non-bonded parameter combinations
832 Generating 1-4 interactions: fudge = 0.5
833 Generated 45 of the 45 1-4 parameter combinations
834 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
835 Excluding 3 bonded neighbours molecule type 'NA'
836 Excluding 3 bonded neighbours molecule type 'CL'
837 Excluding 3 bonded neighbours molecule type 'WAT'
838 Removing all charge groups because cutoff-scheme=Verlet
839
840 NOTE 1 [file morph.top, line 232]:
841 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
842 an estimated oscillational period of 8.0e-03 ps, which is less than 10
843 times the time step of 1.0e-03 ps.
844 Maybe you forgot to change the constraints mdp option.
845
846 Number of degrees of freedom in T-Coupling group System is 12987.00
847 Reading Coordinates, Velocities and Box size from old trajectory
848 Will read whole trajectory
849
850 Last frame -1 time 0.050
851 Using frame at t = 0.05 ps
852 Starting time for run is 0 ps
853 Estimate for the relative computational load of the PME mesh part: 0.23
854
855 There was 1 note
856
857 GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa)
858
859 Analysing residue names:
860 There are: 1 Other residues
861 There are: 10 Ion residues
862 There are: 2151 Water residues
863 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
864 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
865 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
866 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
867 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
868 Note that mdrun will redetermine rlist based on the actual pair-list setup
869 Calculating fourier grid dimensions for X Y Z
870 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
871 This run will generate roughly 1 Mb of data
872 :-) GROMACS - gmx mdrun, 2019.1 (-:
873
874 GROMACS is written by:
875 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
876 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
877 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
878 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
879 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
880 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
881 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
882 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
883 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
884 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
885 Christian Wennberg Maarten Wolf
886 and the project leaders:
887 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
888
889 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
890 Copyright (c) 2001-2018, The GROMACS development team at
891 Uppsala University, Stockholm University and
892 the Royal Institute of Technology, Sweden.
893 check out http://www.gromacs.org for more information.
894
895 GROMACS is free software; you can redistribute it and/or modify it
896 under the terms of the GNU Lesser General Public License
897 as published by the Free Software Foundation; either version 2.1
898 of the License, or (at your option) any later version.
899
900 GROMACS: gmx mdrun, version 2019.1
901 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
902 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
903 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT
904 Command line:
905 gmx mdrun -deffnm npt1
906
907 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
908 The current CPU can measure timings more accurately than the code in
909 gmx mdrun was configured to use. This might affect your simulation
910 speed as accurate timings are needed for load-balancing.
911 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
912 Reading file npt1.tpr, VERSION 2019.1 (single precision)
913 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
914
915
916 Using 1 MPI thread
917 Using 4 OpenMP threads
918
919 starting mdrun 'BioSimSpace System'
920 50 steps, 0.1 ps.
921
922 Writing final coordinates.
923
924 Core t (s) Wall t (s) (%)
925 Time: 1.310 0.328 399.9
926 (ns/day) (hour/ns)
927 Performance: 13.448 1.785
928
929 GROMACS reminds you: "Don't Follow Me Home" (Throwing Muses)
930
931 Constant pressure equilibration complete.
932 Starting production MD simulation...
933 :-) GROMACS - gmx grompp, 2019.1 (-:
934
935 GROMACS is written by:
936 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
937 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
938 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
939 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
940 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
941 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
942 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
943 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
944 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
945 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
946 Christian Wennberg Maarten Wolf
947 and the project leaders:
948 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
949
950 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
951 Copyright (c) 2001-2018, The GROMACS development team at
952 Uppsala University, Stockholm University and
953 the Royal Institute of Technology, Sweden.
954 check out http://www.gromacs.org for more information.
955
956 GROMACS is free software; you can redistribute it and/or modify it
957 under the terms of the GNU Lesser General Public License
958 as published by the Free Software Foundation; either version 2.1
959 of the License, or (at your option) any later version.
960
961 GROMACS: gmx grompp, version 2019.1
962 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
963 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
964 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD
965 Command line:
966 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
967
968
969 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp]:
970 With PME there is a minor soft core effect present at the cut-off,
971 proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
972 energy conservation, but usually other effects dominate. With a common
973 sigma value of 0.34 nm the fraction of the particle-particle potential at
974 the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
975
976 Setting the LD random seed to -651728442
977 Generated 45 of the 45 non-bonded parameter combinations
978 Generating 1-4 interactions: fudge = 0.5
979 Generated 45 of the 45 1-4 parameter combinations
980 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
981 Excluding 3 bonded neighbours molecule type 'NA'
982 Excluding 3 bonded neighbours molecule type 'CL'
983 Excluding 3 bonded neighbours molecule type 'WAT'
984 Removing all charge groups because cutoff-scheme=Verlet
985
986 NOTE 2 [file morph.top, line 232]:
987 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
988 an estimated oscillational period of 8.0e-03 ps, which is less than 10
989 times the time step of 1.0e-03 ps.
990 Maybe you forgot to change the constraints mdp option.
991
992 Number of degrees of freedom in T-Coupling group System is 12987.00
993 Reading Coordinates, Velocities and Box size from old trajectory
994 Will read whole trajectory
995
996 Last frame -1 time 0.050
997 Using frame at t = 0.05 ps
998 Starting time for run is 0 ps
999 Estimate for the relative computational load of the PME mesh part: 0.47
1000
1001 There were 2 notes
1002
1003 GROMACS reminds you: "Beat On the Brat With a Baseball Bat" (The Ramones)
1004
1005 Analysing residue names:
1006 There are: 1 Other residues
1007 There are: 10 Ion residues
1008 There are: 2151 Water residues
1009 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1010 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1011 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
1012 Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
1013 Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
1014 Note that mdrun will redetermine rlist based on the actual pair-list setup
1015 Calculating fourier grid dimensions for X Y Z
1016 Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
1017 This run will generate roughly 1 Mb of data
1018 :-) GROMACS - gmx mdrun, 2019.1 (-:
1019
1020 GROMACS is written by:
1021 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1022 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1023 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1024 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1025 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1026 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1027 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1028 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1029 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1030 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1031 Christian Wennberg Maarten Wolf
1032 and the project leaders:
1033 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1034
1035 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1036 Copyright (c) 2001-2018, The GROMACS development team at
1037 Uppsala University, Stockholm University and
1038 the Royal Institute of Technology, Sweden.
1039 check out http://www.gromacs.org for more information.
1040
1041 GROMACS is free software; you can redistribute it and/or modify it
1042 under the terms of the GNU Lesser General Public License
1043 as published by the Free Software Foundation; either version 2.1
1044 of the License, or (at your option) any later version.
1045
1046 GROMACS: gmx mdrun, version 2019.1
1047 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1048 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1049 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD
1050 Command line:
1051 gmx mdrun -deffnm md1
1052
1053 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
1054 The current CPU can measure timings more accurately than the code in
1055 gmx mdrun was configured to use. This might affect your simulation
1056 speed as accurate timings are needed for load-balancing.
1057 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
1058 Reading file md1.tpr, VERSION 2019.1 (single precision)
1059 Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
1060
1061
1062 Using 1 MPI thread
1063 Using 4 OpenMP threads
1064
1065 starting mdrun 'BioSimSpace System'
1066 2000 steps, 2.0 ps.
1067
1068 Writing final coordinates.
1069
1070 Core t (s) Wall t (s) (%)
1071 Time: 27.548 6.887 400.0
1072 (ns/day) (hour/ns)
1073 Performance: 25.103 0.956
1074
1075 GROMACS reminds you: "Nothing is more anarchic than power." (Pier Paolo Pasolini)
1076
1077 Production MD complete.
1078 Ending. Job completed for lambda = 1
1079 Starting minimization for lambda = 2...
1080 :-) GROMACS - gmx grompp, 2019.1 (-:
1081
1082 GROMACS is written by:
1083 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1084 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1085 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1086 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1087 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1088 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1089 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1090 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1091 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1092 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1093 Christian Wennberg Maarten Wolf
1094 and the project leaders:
1095 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1096
1097 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1098 Copyright (c) 2001-2018, The GROMACS development team at
1099 Uppsala University, Stockholm University and
1100 the Royal Institute of Technology, Sweden.
1101 check out http://www.gromacs.org for more information.
1102
1103 GROMACS is free software; you can redistribute it and/or modify it
1104 under the terms of the GNU Lesser General Public License
1105 as published by the Free Software Foundation; either version 2.1
1106 of the License, or (at your option) any later version.
1107
1108 GROMACS: gmx grompp, version 2019.1
1109 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1110 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1111 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM
1112 Command line:
1113 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
1114
1115 Setting the LD random seed to 886887101
1116 Generated 45 of the 45 non-bonded parameter combinations
1117 Generating 1-4 interactions: fudge = 0.5
1118 Generated 45 of the 45 1-4 parameter combinations
1119 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
1120 Excluding 3 bonded neighbours molecule type 'NA'
1121 Excluding 3 bonded neighbours molecule type 'CL'
1122 Excluding 3 bonded neighbours molecule type 'WAT'
1123 Removing all charge groups because cutoff-scheme=Verlet
1124 Number of degrees of freedom in T-Coupling group rest is 12987.00
1125 Estimate for the relative computational load of the PME mesh part: 0.21
1126
1127 GROMACS reminds you: "Sisters Have Always Fascinated Me" (Speech)
1128
1129 Analysing residue names:
1130 There are: 1 Other residues
1131 There are: 10 Ion residues
1132 There are: 2151 Water residues
1133 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1134 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1135 Calculating fourier grid dimensions for X Y Z
1136 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
1137 This run will generate roughly 1 Mb of data
1138 :-) GROMACS - gmx mdrun, 2019.1 (-:
1139
1140 GROMACS is written by:
1141 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1142 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1143 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1144 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1145 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1146 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1147 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1148 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1149 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1150 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1151 Christian Wennberg Maarten Wolf
1152 and the project leaders:
1153 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1154
1155 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1156 Copyright (c) 2001-2018, The GROMACS development team at
1157 Uppsala University, Stockholm University and
1158 the Royal Institute of Technology, Sweden.
1159 check out http://www.gromacs.org for more information.
1160
1161 GROMACS is free software; you can redistribute it and/or modify it
1162 under the terms of the GNU Lesser General Public License
1163 as published by the Free Software Foundation; either version 2.1
1164 of the License, or (at your option) any later version.
1165
1166 GROMACS: gmx mdrun, version 2019.1
1167 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1168 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1169 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM
1170 Command line:
1171 gmx mdrun -deffnm min2
1172
1173 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
1174 The current CPU can measure timings more accurately than the code in
1175 gmx mdrun was configured to use. This might affect your simulation
1176 speed as accurate timings are needed for load-balancing.
1177 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
1178 Reading file min2.tpr, VERSION 2019.1 (single precision)
1179
1180 Using 1 MPI thread
1181 Using 4 OpenMP threads
1182
1183
1184 Steepest Descents:
1185 Tolerance (Fmax) = 1.00000e+02
1186 Number of steps = 10
1187
1188 Energy minimization reached the maximum number of steps before the forces
1189 reached the requested precision Fmax < 100.
1190
1191 writing lowest energy coordinates.
1192
1193 Steepest Descents did not converge to Fmax < 100 in 11 steps.
1194 Potential Energy = -8.3125391e+04
1195 Maximum force = 2.1372287e+04 on atom 1
1196 Norm of force = 5.1859150e+02
1197
1198 GROMACS reminds you: "The Candlelight Was Just Right" (Beastie Boys)
1199
1200 Starting constant volume equilibration...
1201 :-) GROMACS - gmx grompp, 2019.1 (-:
1202
1203 GROMACS is written by:
1204 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1205 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1206 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1207 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1208 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1209 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1210 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1211 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1212 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1213 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1214 Christian Wennberg Maarten Wolf
1215 and the project leaders:
1216 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1217
1218 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1219 Copyright (c) 2001-2018, The GROMACS development team at
1220 Uppsala University, Stockholm University and
1221 the Royal Institute of Technology, Sweden.
1222 check out http://www.gromacs.org for more information.
1223
1224 GROMACS is free software; you can redistribute it and/or modify it
1225 under the terms of the GNU Lesser General Public License
1226 as published by the Free Software Foundation; either version 2.1
1227 of the License, or (at your option) any later version.
1228
1229 GROMACS: gmx grompp, version 2019.1
1230 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1231 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1232 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT
1233 Command line:
1234 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
1235
1236 Setting the LD random seed to -902054215
1237 Generated 45 of the 45 non-bonded parameter combinations
1238 Generating 1-4 interactions: fudge = 0.5
1239 Generated 45 of the 45 1-4 parameter combinations
1240 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
1241 Excluding 3 bonded neighbours molecule type 'NA'
1242 Excluding 3 bonded neighbours molecule type 'CL'
1243 Excluding 3 bonded neighbours molecule type 'WAT'
1244 Velocities were taken from a Maxwell distribution at 300 K
1245 Removing all charge groups because cutoff-scheme=Verlet
1246
1247 NOTE 1 [file morph.top, line 232]:
1248 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
1249 an estimated oscillational period of 8.0e-03 ps, which is less than 10
1250 times the time step of 1.0e-03 ps.
1251 Maybe you forgot to change the constraints mdp option.
1252
1253 Number of degrees of freedom in T-Coupling group System is 12987.00
1254 Estimate for the relative computational load of the PME mesh part: 0.23
1255
1256 There was 1 note
1257
1258 GROMACS reminds you: "I spent a lot of money on booze, birds and fast cars. The rest I just squandered." (George Best)
1259
1260 Analysing residue names:
1261 There are: 1 Other residues
1262 There are: 10 Ion residues
1263 There are: 2151 Water residues
1264 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1265 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1266 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
1267 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
1268 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
1269 Note that mdrun will redetermine rlist based on the actual pair-list setup
1270 Calculating fourier grid dimensions for X Y Z
1271 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
1272 This run will generate roughly 1 Mb of data
1273 :-) GROMACS - gmx mdrun, 2019.1 (-:
1274
1275 GROMACS is written by:
1276 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1277 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1278 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1279 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1280 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1281 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1282 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1283 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1284 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1285 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1286 Christian Wennberg Maarten Wolf
1287 and the project leaders:
1288 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1289
1290 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1291 Copyright (c) 2001-2018, The GROMACS development team at
1292 Uppsala University, Stockholm University and
1293 the Royal Institute of Technology, Sweden.
1294 check out http://www.gromacs.org for more information.
1295
1296 GROMACS is free software; you can redistribute it and/or modify it
1297 under the terms of the GNU Lesser General Public License
1298 as published by the Free Software Foundation; either version 2.1
1299 of the License, or (at your option) any later version.
1300
1301 GROMACS: gmx mdrun, version 2019.1
1302 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1303 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1304 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT
1305 Command line:
1306 gmx mdrun -deffnm nvt2
1307
1308 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
1309 The current CPU can measure timings more accurately than the code in
1310 gmx mdrun was configured to use. This might affect your simulation
1311 speed as accurate timings are needed for load-balancing.
1312 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
1313 Reading file nvt2.tpr, VERSION 2019.1 (single precision)
1314 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
1315
1316
1317 Using 1 MPI thread
1318 Using 4 OpenMP threads
1319
1320 starting mdrun 'BioSimSpace System'
1321 50 steps, 0.1 ps.
1322
1323 Writing final coordinates.
1324
1325 Core t (s) Wall t (s) (%)
1326 Time: 1.308 0.327 399.9
1327 (ns/day) (hour/ns)
1328 Performance: 13.471 1.782
1329
1330 GROMACS reminds you: "What if you're wrong about the great Ju Ju at the bottom of the sea?" (Richard Dawkins)
1331
1332 Constant volume equilibration complete.
1333 Starting constant pressure equilibration...
1334 :-) GROMACS - gmx grompp, 2019.1 (-:
1335
1336 GROMACS is written by:
1337 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1338 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1339 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1340 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1341 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1342 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1343 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1344 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1345 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1346 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1347 Christian Wennberg Maarten Wolf
1348 and the project leaders:
1349 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1350
1351 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1352 Copyright (c) 2001-2018, The GROMACS development team at
1353 Uppsala University, Stockholm University and
1354 the Royal Institute of Technology, Sweden.
1355 check out http://www.gromacs.org for more information.
1356
1357 GROMACS is free software; you can redistribute it and/or modify it
1358 under the terms of the GNU Lesser General Public License
1359 as published by the Free Software Foundation; either version 2.1
1360 of the License, or (at your option) any later version.
1361
1362 GROMACS: gmx grompp, version 2019.1
1363 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1364 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1365 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT
1366 Command line:
1367 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
1368
1369 Setting the LD random seed to -652502066
1370 Generated 45 of the 45 non-bonded parameter combinations
1371 Generating 1-4 interactions: fudge = 0.5
1372 Generated 45 of the 45 1-4 parameter combinations
1373 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
1374 Excluding 3 bonded neighbours molecule type 'NA'
1375 Excluding 3 bonded neighbours molecule type 'CL'
1376 Excluding 3 bonded neighbours molecule type 'WAT'
1377 Removing all charge groups because cutoff-scheme=Verlet
1378
1379 NOTE 1 [file morph.top, line 232]:
1380 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
1381 an estimated oscillational period of 8.0e-03 ps, which is less than 10
1382 times the time step of 1.0e-03 ps.
1383 Maybe you forgot to change the constraints mdp option.
1384
1385 Number of degrees of freedom in T-Coupling group System is 12987.00
1386 Reading Coordinates, Velocities and Box size from old trajectory
1387 Will read whole trajectory
1388
1389 Last frame -1 time 0.050
1390 Using frame at t = 0.05 ps
1391 Starting time for run is 0 ps
1392 Estimate for the relative computational load of the PME mesh part: 0.23
1393
1394 There was 1 note
1395
1396 GROMACS reminds you: "When doing HPC, don't communica" (Jim Demmel)
1397
1398 Analysing residue names:
1399 There are: 1 Other residues
1400 There are: 10 Ion residues
1401 There are: 2151 Water residues
1402 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1403 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1404 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
1405 Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
1406 Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
1407 Note that mdrun will redetermine rlist based on the actual pair-list setup
1408 Calculating fourier grid dimensions for X Y Z
1409 Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
1410 This run will generate roughly 1 Mb of data
1411 :-) GROMACS - gmx mdrun, 2019.1 (-:
1412
1413 GROMACS is written by:
1414 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1415 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1416 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1417 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1418 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1419 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1420 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1421 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1422 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1423 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1424 Christian Wennberg Maarten Wolf
1425 and the project leaders:
1426 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1427
1428 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1429 Copyright (c) 2001-2018, The GROMACS development team at
1430 Uppsala University, Stockholm University and
1431 the Royal Institute of Technology, Sweden.
1432 check out http://www.gromacs.org for more information.
1433
1434 GROMACS is free software; you can redistribute it and/or modify it
1435 under the terms of the GNU Lesser General Public License
1436 as published by the Free Software Foundation; either version 2.1
1437 of the License, or (at your option) any later version.
1438
1439 GROMACS: gmx mdrun, version 2019.1
1440 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1441 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1442 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT
1443 Command line:
1444 gmx mdrun -deffnm npt2
1445
1446 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
1447 The current CPU can measure timings more accurately than the code in
1448 gmx mdrun was configured to use. This might affect your simulation
1449 speed as accurate timings are needed for load-balancing.
1450 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
1451 Reading file npt2.tpr, VERSION 2019.1 (single precision)
1452 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
1453
1454
1455 Using 1 MPI thread
1456 Using 4 OpenMP threads
1457
1458 starting mdrun 'BioSimSpace System'
1459 50 steps, 0.1 ps.
1460
1461 Writing final coordinates.
1462
1463 Core t (s) Wall t (s) (%)
1464 Time: 1.290 0.323 399.9
1465 (ns/day) (hour/ns)
1466 Performance: 13.659 1.757
1467
1468 GROMACS reminds you: "People are DNA's way of making more DNA." (Edward O. Wilson)
1469
1470 Constant pressure equilibration complete.
1471 Starting production MD simulation...
1472 :-) GROMACS - gmx grompp, 2019.1 (-:
1473
1474 GROMACS is written by:
1475 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1476 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1477 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1478 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1479 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1480 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1481 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1482 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1483 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1484 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1485 Christian Wennberg Maarten Wolf
1486 and the project leaders:
1487 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1488
1489 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1490 Copyright (c) 2001-2018, The GROMACS development team at
1491 Uppsala University, Stockholm University and
1492 the Royal Institute of Technology, Sweden.
1493 check out http://www.gromacs.org for more information.
1494
1495 GROMACS is free software; you can redistribute it and/or modify it
1496 under the terms of the GNU Lesser General Public License
1497 as published by the Free Software Foundation; either version 2.1
1498 of the License, or (at your option) any later version.
1499
1500 GROMACS: gmx grompp, version 2019.1
1501 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1502 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1503 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD
1504 Command line:
1505 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
1506
1507
1508 NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp]:
1509 With PME there is a minor soft core effect present at the cut-off,
1510 proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
1511 energy conservation, but usually other effects dominate. With a common
1512 sigma value of 0.34 nm the fraction of the particle-particle potential at
1513 the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
1514
1515 Setting the LD random seed to 551042888
1516 Generated 45 of the 45 non-bonded parameter combinations
1517 Generating 1-4 interactions: fudge = 0.5
1518 Generated 45 of the 45 1-4 parameter combinations
1519 Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
1520 Excluding 3 bonded neighbours molecule type 'NA'
1521 Excluding 3 bonded neighbours molecule type 'CL'
1522 Excluding 3 bonded neighbours molecule type 'WAT'
1523 Removing all charge groups because cutoff-scheme=Verlet
1524
1525 NOTE 2 [file morph.top, line 232]:
1526 The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
1527 an estimated oscillational period of 8.0e-03 ps, which is less than 10
1528 times the time step of 1.0e-03 ps.
1529 Maybe you forgot to change the constraints mdp option.
1530
1531 Number of degrees of freedom in T-Coupling group System is 12987.00
1532 Reading Coordinates, Velocities and Box size from old trajectory
1533 Will read whole trajectory
1534
1535 Last frame -1 time 0.050
1536 Using frame at t = 0.05 ps
1537 Starting time for run is 0 ps
1538 Estimate for the relative computational load of the PME mesh part: 0.47
1539
1540 There were 2 notes
1541
1542 GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)
1543
1544 Analysing residue names:
1545 There are: 1 Other residues
1546 There are: 10 Ion residues
1547 There are: 2151 Water residues
1548 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1549 Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
1550 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
1551 Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
1552 Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
1553 Note that mdrun will redetermine rlist based on the actual pair-list setup
1554 Calculating fourier grid dimensions for X Y Z
1555 Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
1556 This run will generate roughly 1 Mb of data
1557 :-) GROMACS - gmx mdrun, 2019.1 (-:
1558
1559 GROMACS is written by:
1560 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
1561 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
1562 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
1563 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
1564 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
1565 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
1566 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
1567 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
1568 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
1569 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
1570 Christian Wennberg Maarten Wolf
1571 and the project leaders:
1572 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
1573
1574 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
1575 Copyright (c) 2001-2018, The GROMACS development team at
1576 Uppsala University, Stockholm University and
1577 the Royal Institute of Technology, Sweden.
1578 check out http://www.gromacs.org for more information.
1579
1580 GROMACS is free software; you can redistribute it and/or modify it
1581 under the terms of the GNU Lesser General Public License
1582 as published by the Free Software Foundation; either version 2.1
1583 of the License, or (at your option) any later version.
1584
1585 GROMACS: gmx mdrun, version 2019.1
1586 Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
1587 Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
1588 Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD
1589 Command line:
1590 gmx mdrun -deffnm md2
1591
1592 Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
1593 The current CPU can measure timings more accurately than the code in
1594 gmx mdrun was configured to use. This might affect your simulation
1595 speed as accurate timings are needed for load-balancing.
1596 Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
1597 Reading file md2.tpr, VERSION 2019.1 (single precision)
1598 Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
1599
1600
1601 Using 1 MPI thread
1602 Using 4 OpenMP threads
1603
1604 starting mdrun 'BioSimSpace System'
1605 2000 steps, 2.0 ps.
1606
1607 step 2: One or more water molecules can not be settled.
1608 Check for bad contacts and/or reduce the timestep if appropriate.
1609 Wrote pdb files with previous and current coordinates
1610
1611 WARNING: Listed nonbonded interaction between particles 6 and 15
1612 at distance 47.750 which is larger than the table limit 1.860 nm.
1613
1614 This is likely either a 1,4 interaction, or a listed interaction inside
1615 a smaller molecule you are decoupling during a free energy calculation.
1616 Since interactions at distances beyond the table cannot be computed,
1617 they are skipped until they are inside the table limit again. You will
1618 only see this message once, even if it occurs for several interactions.
1619
1620 IMPORTANT: This should not happen in a stable simulation, so there is
1621 probably something wrong with your system. Only change the table-extension
1622 distance in the mdp file if you are really sure that is the reason.
1623
1624
1625
1626 WARNING: Listed nonbonded interaction between particles 2 and 15
1627 at distance 47.627 which is larger than the table limit 1.860 nm.
1628
1629 This is likely either a 1,4 interaction, or a listed interaction inside
1630 a smaller molecule you are decoupling during a free energy calculation.
1631 Since interactions at distances beyond the table cannot be computed,
1632 they are skipped until they are inside the table limit again. You will
1633 only see this message once, even if it occurs for several interactions.
1634
1635 IMPORTANT: This should not happen in a stable simulation, so there is
1636 probably something wrong with your system. Only change the table-extension
1637 distance in the mdp file if you are really sure that is the reason.
1638
1639
1640 /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
1641 Production MD complete.
1642 Ending. Job completed for lambda = 2