Mercurial > repos > chemteam > alchemical_analysis
diff 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 |
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| date | Mon, 18 Nov 2019 09:52:20 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/test-data/Report.txt Mon Nov 18 09:52:20 2019 -0500 @@ -0,0 +1,1636 @@ +Starting minimization for lambda = 0... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_0.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min0.tpr + +Setting the LD random seed to -127141127 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet +Number of degrees of freedom in T-Coupling group rest is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.21 + +GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM +Command line: + gmx mdrun -deffnm min0 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file min0.tpr, VERSION 2019.1 (single precision) + +Using 1 MPI thread +Using 4 OpenMP threads + + +Steepest Descents: + Tolerance (Fmax) = 1.00000e+02 + Number of steps = 10 + +Energy minimization reached the maximum number of steps before the forces +reached the requested precision Fmax < 100. + +writing lowest energy coordinates. + +Steepest Descents did not converge to Fmax < 100 in 11 steps. +Potential Energy = -8.3125391e+04 +Maximum force = 2.1372287e+04 on atom 1 +Norm of force = 5.1859150e+02 + +GROMACS reminds you: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." (Watson & Crick) + +Starting constant volume equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_0.mdp -c ../EM/min0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt0.tpr + +Setting the LD random seed to -187712966 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Velocities were taken from a Maxwell distribution at 300 K +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "Nada e organico, e tudo programado" (Pitty) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT +Command line: + gmx mdrun -deffnm nvt0 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file nvt0.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.458 0.365 399.9 + (ns/day) (hour/ns) +Performance: 12.084 1.986 + +GROMACS reminds you: "I Quit My Job Blowing Leaves" (Beck) + +Constant volume equilibration complete. +Starting constant pressure equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_0.mdp -c ../NVT/nvt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt0.cpt -o npt0.tpr + +Setting the LD random seed to 2038796930 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "Act like Prometheus would" (Gogol Bordello) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT +Command line: + gmx mdrun -deffnm npt0 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file npt0.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.261 0.315 399.9 + (ns/day) (hour/ns) +Performance: 13.979 1.717 + +GROMACS reminds you: "I Was Born to Have Adventure" (F. Zappa) + +Constant pressure equilibration complete. +Starting production MD simulation... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp -c ../NPT/npt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt0.cpt -o md0.tpr + + +NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp]: + With PME there is a minor soft core effect present at the cut-off, + proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on + energy conservation, but usually other effects dominate. With a common + sigma value of 0.34 nm the fraction of the particle-particle potential at + the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. + +Setting the LD random seed to -1773803540 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 2 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.47 + +There were 2 notes + +GROMACS reminds you: "God is a DJ" (Faithless) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm +Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD +Command line: + gmx mdrun -deffnm md0 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file md0.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +2000 steps, 2.0 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 27.033 6.758 400.0 + (ns/day) (hour/ns) +Performance: 25.581 0.938 + +GROMACS reminds you: "Don't You Wish You Never Met Her, Dirty Blue Gene?" (Captain Beefheart) + +Production MD complete. +Ending. Job completed for lambda = 0 +Starting minimization for lambda = 1... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_1.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min1.tpr + +Setting the LD random seed to -1393309481 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet +Number of degrees of freedom in T-Coupling group rest is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.21 + +GROMACS reminds you: "Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia." (Roald Hoffmann) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM +Command line: + gmx mdrun -deffnm min1 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file min1.tpr, VERSION 2019.1 (single precision) + +Using 1 MPI thread +Using 4 OpenMP threads + + +Steepest Descents: + Tolerance (Fmax) = 1.00000e+02 + Number of steps = 10 + +Energy minimization reached the maximum number of steps before the forces +reached the requested precision Fmax < 100. + +writing lowest energy coordinates. + +Steepest Descents did not converge to Fmax < 100 in 11 steps. +Potential Energy = -8.3125391e+04 +Maximum force = 2.1372287e+04 on atom 1 +Norm of force = 5.1859150e+02 + +GROMACS reminds you: "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie" (Lola rennt) + +Starting constant volume equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_1.mdp -c ../EM/min1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt1.tpr + +Setting the LD random seed to -1631510067 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Velocities were taken from a Maxwell distribution at 300 K +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "No great discovery was ever made without a bold guess." (Marie Curie) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT +Command line: + gmx mdrun -deffnm nvt1 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file nvt1.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.273 0.318 399.9 + (ns/day) (hour/ns) +Performance: 13.842 1.734 + +GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter) + +Constant volume equilibration complete. +Starting constant pressure equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_1.mdp -c ../NVT/nvt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt1.cpt -o npt1.tpr + +Setting the LD random seed to -166230178 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT +Command line: + gmx mdrun -deffnm npt1 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file npt1.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.310 0.328 399.9 + (ns/day) (hour/ns) +Performance: 13.448 1.785 + +GROMACS reminds you: "Don't Follow Me Home" (Throwing Muses) + +Constant pressure equilibration complete. +Starting production MD simulation... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp -c ../NPT/npt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt1.cpt -o md1.tpr + + +NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp]: + With PME there is a minor soft core effect present at the cut-off, + proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on + energy conservation, but usually other effects dominate. With a common + sigma value of 0.34 nm the fraction of the particle-particle potential at + the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. + +Setting the LD random seed to -651728442 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 2 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.47 + +There were 2 notes + +GROMACS reminds you: "Beat On the Brat With a Baseball Bat" (The Ramones) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm +Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD +Command line: + gmx mdrun -deffnm md1 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file md1.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +2000 steps, 2.0 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 27.548 6.887 400.0 + (ns/day) (hour/ns) +Performance: 25.103 0.956 + +GROMACS reminds you: "Nothing is more anarchic than power." (Pier Paolo Pasolini) + +Production MD complete. +Ending. Job completed for lambda = 1 +Starting minimization for lambda = 2... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_2.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min2.tpr + +Setting the LD random seed to 886887101 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet +Number of degrees of freedom in T-Coupling group rest is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.21 + +GROMACS reminds you: "Sisters Have Always Fascinated Me" (Speech) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM +Command line: + gmx mdrun -deffnm min2 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file min2.tpr, VERSION 2019.1 (single precision) + +Using 1 MPI thread +Using 4 OpenMP threads + + +Steepest Descents: + Tolerance (Fmax) = 1.00000e+02 + Number of steps = 10 + +Energy minimization reached the maximum number of steps before the forces +reached the requested precision Fmax < 100. + +writing lowest energy coordinates. + +Steepest Descents did not converge to Fmax < 100 in 11 steps. +Potential Energy = -8.3125391e+04 +Maximum force = 2.1372287e+04 on atom 1 +Norm of force = 5.1859150e+02 + +GROMACS reminds you: "The Candlelight Was Just Right" (Beastie Boys) + +Starting constant volume equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_2.mdp -c ../EM/min2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt2.tpr + +Setting the LD random seed to -902054215 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Velocities were taken from a Maxwell distribution at 300 K +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "I spent a lot of money on booze, birds and fast cars. The rest I just squandered." (George Best) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT +Command line: + gmx mdrun -deffnm nvt2 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file nvt2.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.308 0.327 399.9 + (ns/day) (hour/ns) +Performance: 13.471 1.782 + +GROMACS reminds you: "What if you're wrong about the great Ju Ju at the bottom of the sea?" (Richard Dawkins) + +Constant volume equilibration complete. +Starting constant pressure equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_2.mdp -c ../NVT/nvt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt2.cpt -o npt2.tpr + +Setting the LD random seed to -652502066 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "When doing HPC, don't communica" (Jim Demmel) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT +Command line: + gmx mdrun -deffnm npt2 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file npt2.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.290 0.323 399.9 + (ns/day) (hour/ns) +Performance: 13.659 1.757 + +GROMACS reminds you: "People are DNA's way of making more DNA." (Edward O. Wilson) + +Constant pressure equilibration complete. +Starting production MD simulation... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp -c ../NPT/npt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt2.cpt -o md2.tpr + + +NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp]: + With PME there is a minor soft core effect present at the cut-off, + proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on + energy conservation, but usually other effects dominate. With a common + sigma value of 0.34 nm the fraction of the particle-particle potential at + the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. + +Setting the LD random seed to 551042888 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 2 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.47 + +There were 2 notes + +GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm +Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD +Command line: + gmx mdrun -deffnm md2 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file md2.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +2000 steps, 2.0 ps. + +step 2: One or more water molecules can not be settled. +Check for bad contacts and/or reduce the timestep if appropriate. +Wrote pdb files with previous and current coordinates + +WARNING: Listed nonbonded interaction between particles 6 and 15 +at distance 47.750 which is larger than the table limit 1.860 nm. + +This is likely either a 1,4 interaction, or a listed interaction inside +a smaller molecule you are decoupling during a free energy calculation. +Since interactions at distances beyond the table cannot be computed, +they are skipped until they are inside the table limit again. You will +only see this message once, even if it occurs for several interactions. + +IMPORTANT: This should not happen in a stable simulation, so there is +probably something wrong with your system. Only change the table-extension +distance in the mdp file if you are really sure that is the reason. + + + +WARNING: Listed nonbonded interaction between particles 2 and 15 +at distance 47.627 which is larger than the table limit 1.860 nm. + +This is likely either a 1,4 interaction, or a listed interaction inside +a smaller molecule you are decoupling during a free energy calculation. +Since interactions at distances beyond the table cannot be computed, +they are skipped until they are inside the table limit again. You will +only see this message once, even if it occurs for several interactions. + +IMPORTANT: This should not happen in a stable simulation, so there is +probably something wrong with your system. Only change the table-extension +distance in the mdp file if you are really sure that is the reason. + + +/scratch2/tsenapathi/Projects/BRIDGE/galaxy-tools-compchem/tools/free_energy/alchemical_run/gmx_fep.sh: line 104: 13890 Segmentation fault gmx mdrun -deffnm md$LAMBDA +Production MD complete. +Ending. Job completed for lambda = 2