Mercurial > repos > chemteam > alchemical_analysis
comparison alchemical_run/test-data/Report.txt @ 0:5f136e371f44 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit 4c75f8d26505d221d4144f4ae7d2fb7698fbe4ab"
| author | chemteam |
|---|---|
| date | Mon, 18 Nov 2019 09:52:20 -0500 |
| parents | |
| children |
comparison
equal
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| -1:000000000000 | 0:5f136e371f44 |
|---|---|
| 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 |