tsenapathi
commented
5 years ago @simonbray Thanks!
Closed tsenapathi closed 4 years ago
tsenapathi
commented
5 years ago @simonbray Thanks!
tsenapathi
commented
5 years ago ping @simonbray
simonbray
commented
5 years ago you could move this tool to the gromacs folder, but I don't have a strong opinion about that.
simonbray
commented
5 years ago Don't know very much about alchemical free energy calculations but isn't it typical to add constraints in the NVT/NPT equilibration steps and then remove them in the final simulation?
tsenapathi
commented
5 years ago @simonbray I have a few more tools to setup and analysis of free energy calculations and I tought keep them together. That's why I made a separate folder for that. I can move the tool to the Gromacs folder @chrisbarnettster what you think?
tsenapathi
commented
5 years ago @simonbray Yes, Alchemical free energy simulations use a set of nonphysical (alchemical) states to perturb one molecule to another. These alchemical states are not binding to proteins as normal ligands and tend to move away from the active site. So we must use a restraint.
The Pre equilibration is nesseosory to remove hamiltonian laggings from the previous simulations to achieve good phase space overlap for correct free energy estimation in a finite simulation.
simonbray
commented
5 years ago But you have an option not to apply constraints. I'm wondering if this is really necessary, or if it should at least be compulsory to restrain the ligand in the equilibration stage
simonbray
commented
5 years ago Add a .shed.yml file? (not necessary if you move to the gromacs folder though, let's wait and see what @chrisbarnettster has to say)
bgruening
commented
5 years ago If you add a shed.yml and you plan to add more tools, please make sure to use a suite-based-shed.yml
tsenapathi
commented
5 years ago @simonbray How can I add a web site in the citation section?
simonbray
commented
5 years ago I would do <citation type="bibtex"> with a bibtex entry for the website.
tsenapathi
commented
4 years ago @bgruening @simonbray Thanks for your comments and suggestions! The tool has improved significantly.
simonbray
commented
4 years ago @tsenapathi can you add help text to the parameters please? (I guess things like temperature and pressure don't need them, but the rest do.)
tsenapathi
commented
4 years ago @simonbray @bgruening @chrisbarnettster anymore suggestions? or can we merge?
simonbray
commented
4 years ago @tsenapathi, I added a few small suggestions and some more help text for LINCS parameters. Otherwise this looks good to me, thanks!
simonbray
commented
4 years ago @chrisbarnettster could you also take a quick look from a technical point of view? I don't know very much about FEP.
tsenapathi
commented
4 years ago Thanks @simonbray updated!
simonbray
commented
4 years ago you can also accept the suggestions directly in github if you like :)
simonbray
commented
4 years ago @tsenapathi another question I'm afraid... I ran the tool to generate input files and tested out ./gmx_fep.sh, but it throws a lot of errors. Can you try this out and work out how to fix it?
tsenapathi
commented
4 years ago @simonbray you need to specify the number of windows as an argument
./gmx_fep.sh 40
tsenapathi
commented
4 years ago @simonbray try this and let me know if there are any problems.
chrisbarnettster
commented
4 years ago taking a look over today/tomorrow
simonbray
commented
4 years ago I tried that too, it also doesn't work
tsenapathi
commented
4 years ago Try the .top and .gro files in the test data or Input_files.tar
tsenapathi
commented
4 years ago @simonbray I have tested them now, seems working for me.
simonbray
commented
4 years ago Here are the errors I get with the test-data:
(gmx) simon@simon-notebook:~/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files$ bash gmx_fep.sh 2
mkdir: cannot create directory ‘MDP’: File exists
mkdir: cannot create directory ‘data’: File exists
mkdir: cannot create directory ‘traj’: File exists
cp: cannot stat 'em_steep.mdp': No such file or directory
sed: can't read em_steep_0.mdp: No such file or directory
cp: cannot stat 'nvt.mdp': No such file or directory
sed: can't read nvt_0.mdp: No such file or directory
cp: cannot stat 'npt.mdp': No such file or directory
sed: can't read npt_0.mdp: No such file or directory
cp: cannot stat 'md.mdp': No such file or directory
sed: can't read md_0.mdp: No such file or directory
cp: cannot stat 'em_steep.mdp': No such file or directory
sed: can't read em_steep_1.mdp: No such file or directory
cp: cannot stat 'nvt.mdp': No such file or directory
sed: can't read nvt_1.mdp: No such file or directory
cp: cannot stat 'npt.mdp': No such file or directory
sed: can't read npt_1.mdp: No such file or directory
cp: cannot stat 'md.mdp': No such file or directory
sed: can't read md_1.mdp: No such file or directory
cp: cannot stat 'em_steep.mdp': No such file or directory
sed: can't read em_steep_2.mdp: No such file or directory
cp: cannot stat 'nvt.mdp': No such file or directory
sed: can't read nvt_2.mdp: No such file or directory
cp: cannot stat 'npt.mdp': No such file or directory
sed: can't read npt_2.mdp: No such file or directory
cp: cannot stat 'md.mdp': No such file or directory
sed: can't read md_2.mdp: No such file or directory
mv: cannot stat '*.mdp': No such file or directory
mkdir: cannot create directory ‘Lambda_0’: File exists
Starting minimization for lambda = 0...
mkdir: cannot create directory ‘EM’: File exists
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_0/EM
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/em_steep_0.mdp -c /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -o min0.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/em_steep_0.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_0/EM
Command line:
gmx mdrun -deffnm min0
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Starting constant volume equilibration...
mkdir: cannot create directory ‘NVT’: File exists
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_0/NVT
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/nvt_0.mdp -c ../EM/min0.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -o nvt0.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/nvt_0.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../EM/min0.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_0/NVT
Command line:
gmx mdrun -deffnm nvt0
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Constant volume equilibration complete.
Starting constant pressure equilibration...
mkdir: cannot create directory ‘NPT’: File exists
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_0/NPT
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/npt_0.mdp -c ../NVT/nvt0.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -t ../NVT/nvt0.cpt -o npt0.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/npt_0.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../NVT/nvt0.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -t
File '../NVT/nvt0.cpt' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_0/NPT
Command line:
gmx mdrun -deffnm npt0
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Constant pressure equilibration complete.
Starting production MD simulation...
mkdir: cannot create directory ‘Production_MD’: File exists
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_0/Production_MD
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/md_0.mdp -c ../NPT/npt0.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -t ../NPT/npt0.cpt -o md0.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/md_0.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../NPT/npt0.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -t
File '../NPT/npt0.cpt' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_0/Production_MD
Command line:
gmx mdrun -deffnm md0
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_1/EM
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/em_steep_1.mdp -c /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -o min1.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/em_steep_1.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_1/EM
Command line:
gmx mdrun -deffnm min1
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_1/NVT
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/nvt_1.mdp -c ../EM/min1.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -o nvt1.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/nvt_1.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../EM/min1.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_1/NVT
Command line:
gmx mdrun -deffnm nvt1
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_1/NPT
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/npt_1.mdp -c ../NVT/nvt1.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -t ../NVT/nvt1.cpt -o npt1.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/npt_1.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../NVT/nvt1.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -t
File '../NVT/nvt1.cpt' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_1/NPT
Command line:
gmx mdrun -deffnm npt1
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_1/Production_MD
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/md_1.mdp -c ../NPT/npt1.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -t ../NPT/npt1.cpt -o md1.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/md_1.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../NPT/npt1.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -t
File '../NPT/npt1.cpt' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_1/Production_MD
Command line:
gmx mdrun -deffnm md1
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_2/EM
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/em_steep_2.mdp -c /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -o min2.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/em_steep_2.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_2/EM
Command line:
gmx mdrun -deffnm min2
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_2/NVT
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/nvt_2.mdp -c ../EM/min2.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -o nvt2.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/nvt_2.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../EM/min2.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_2/NVT
Command line:
gmx mdrun -deffnm nvt2
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_2/NPT
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/npt_2.mdp -c ../NVT/nvt2.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -t ../NVT/nvt2.cpt -o npt2.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/npt_2.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../NVT/nvt2.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -t
File '../NVT/nvt2.cpt' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_2/NPT
Command line:
gmx mdrun -deffnm npt2
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_2/Production_MD
Command line:
gmx grompp -f /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/md_2.mdp -c ../NPT/npt2.gro -p /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/morph.top -t ../NPT/npt2.cpt -o md2.tpr
-------------------------------------------------------
Program: gmx grompp, version 2019.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File
'/home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/MDP/md_2.mdp'
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '../NPT/npt2.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -t
File '../NPT/npt2.cpt' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
:-) 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/simon/miniconda3/envs/gmx/bin/gmx
Data prefix: /home/simon/miniconda3/envs/gmx
Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/free_energy/alchemical_run/test-data/input_files/Lambda_2/Production_MD
Command line:
gmx mdrun -deffnm md2
-------------------------------------------------------
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/options/options.cpp (line 190)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Production MD complete.
Ending. Job completed for lambda = 2
cp: cannot stat 'Lambda_*/Production_MD/*.xvg': No such file or directory
cp: cannot stat 'Lambda_*/Production_MD/*.trr': No such file or directory
Can you see the .mdp files in the MDP directory. IF not untar the Input_files.tar again and run ./gmx_fep.sh 2
tsenapathi
commented
4 years ago Sorry ./gmx_fep.sh 40
tsenapathi
commented
4 years ago @simonbray is it working?
simonbray
commented
4 years ago I tried again from scratch, after deleting input_files and untarring again. And it seems to work, also with my own test data. Thanks! :)
tsenapathi
commented
4 years ago @simonbray Great!
bgruening
commented
4 years ago It is already green, just github has not updated the status.
tsenapathi
commented
4 years ago @bgruening good to merge?
bgruening
commented
4 years ago Jupp! Can you add it to usegalaxy.eu?
tsenapathi
commented
4 years ago Thanks! I will add this tomorrow.
simonbray
commented
4 years ago @chrisbarnettster a quick check would still be nice if you have time
simonbray
commented
4 years ago Actually one more thing that I only noticed after the merge: it would be nice to put set -e at the start of gmx_fep.sh. Currently one of the intermediate jobs can fail but the job still comes back as green, which is quite confusing for the user when the output files are empty.
tsenapathi
commented
4 years ago @simonbray whare should I put set -e?
simonbray
commented
4 years ago At the start of gmx_fep.sh
Looks amazing @tsenapathi! Will try and review tomorrow afternoon.