Polymeric lithium ion battery Example

[rdguerrerom]

Dear all,

I am working on simulating ion conduction in lithium-ion batteries, and I came across a reference that suggests using polyply to create the initial coordinates for the simulation. While I have gone through the tutorial, I am having trouble to understand fuly the protocol for generating the structures in panels A and B of Figure 4 in the paper as reported here. I would greatly appreciate any assistance or guidance to fully understand how to generate these structures using polyply.

Thank you very much in advance for your help.

Currently, I have installed GROMACS and polyply. I don't know how to set up Martini.

The following are the error messages I get when I try to run the protocol:

$ bash protocol.sh
protocol.sh: line 5: find_path: command not found
INFO - step - reading input and library files
INFO - step - reading sequence from command
INFO - step - mapping sequence to molecule
INFO - step - applying links between residues
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 65/65 [00:00<00:00, 158.14it/s]
INFO - general - Please cite: Grunewald, F; Alessandri, R; Kroon, P C; Monticelli, L; Souza, P C; Marrink, S J;  Nature Communications 2022; 10.1038/s41467-021-27627-4
INFO - general - Please cite: Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J;  Nature Methods 2021; 10.1038/s41592-021-01098-3
INFO - step - reading topology
Traceback (most recent call last):
  File "/Users/ruben/opt/anaconda3/bin/polyply", line 258, in <module>
    main()
  File "/Users/ruben/opt/anaconda3/bin/polyply", line 254, in main
    subprogram(**args_dict)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/gen_coords.py", line 195, in gen_coords
    topology = Topology.from_gmx_topfile(name=name, path=toppath)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/topology.py", line 506, in from_gmx_topfile
    read_topology(lines=lines, topology=topology, cwdir=cwdir)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/top_parser.py", line 504, in read_topology
    return list(director.parse(iter(lines)))
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/vermouth/parser_utils.py", line 110, in parse
    result = self.dispatch(line)(line, lineno)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/top_parser.py", line 189, in parse_top_pragma
    action(line)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/top_parser.py", line 445, in parse_include
    raise IOError(msg.format(filename))
OSError: Cannot find file /martini3/martini_v3.0.0.itp. This can happen when you 1) typed the path to the file wrongly or 2) when you try to include force-field files from the GMX library (e.g. #include "gromos"). Instead provide the full path. Another source for this error can be that you have a #ifdef section with an #include but your include file does not exist. In that case if you don't have the file remove the #include statement.
INFO - step - reading topology
Traceback (most recent call last):
  File "/Users/ruben/opt/anaconda3/bin/polyply", line 258, in <module>
    main()
  File "/Users/ruben/opt/anaconda3/bin/polyply", line 254, in main
    subprogram(**args_dict)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/gen_coords.py", line 195, in gen_coords
    topology = Topology.from_gmx_topfile(name=name, path=toppath)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/topology.py", line 506, in from_gmx_topfile
    read_topology(lines=lines, topology=topology, cwdir=cwdir)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/top_parser.py", line 504, in read_topology
    return list(director.parse(iter(lines)))
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/vermouth/parser_utils.py", line 110, in parse
    result = self.dispatch(line)(line, lineno)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/top_parser.py", line 189, in parse_top_pragma
    action(line)
  File "/Users/ruben/opt/anaconda3/lib/python3.9/site-packages/polyply/src/top_parser.py", line 445, in parse_include
    raise IOError(msg.format(filename))
OSError: Cannot find file /martini3/martini_v3.0.0.itp. This can happen when you 1) typed the path to the file wrongly or 2) when you try to include force-field files from the GMX library (e.g. #include "gromos"). Instead provide the full path. Another source for this error can be that you have a #ifdef section with an #include but your include file does not exist. In that case if you don't have the file remove the #include statement.
                       :-) GROMACS - gmx grompp, 2023 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/example_battery
Command line:
  gmx grompp -f /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/input/min.mdp -c polymers.gro -p system.top


-------------------------------------------------------
Program:     gmx grompp, version 2023
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -c
    File 'polymers.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, 2023 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/example_battery
Command line:
  gmx mdrun -v


-------------------------------------------------------
Program:     gmx mdrun, version 2023
Source file: src/gromacs/options/options.cpp (line 177)
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
-------------------------------------------------------
                       :-) GROMACS - gmx grompp, 2023 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/example_battery
Command line:
  gmx grompp -f /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/input/constz_flex.mdp -c polymers.gro -p system.top


-------------------------------------------------------
Program:     gmx grompp, version 2023
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -c
    File 'polymers.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, 2023 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/example_battery
Command line:
  gmx mdrun -v


-------------------------------------------------------
Program:     gmx mdrun, version 2023
Source file: src/gromacs/options/options.cpp (line 177)
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
-------------------------------------------------------
                       :-) GROMACS - gmx grompp, 2023 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/example_battery
Command line:
  gmx grompp -f /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/input/constz.mdp -c confout.gro -p system.top


-------------------------------------------------------
Program:     gmx grompp, version 2023
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
    File
    '/Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/input/constz.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 'confout.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, 2023 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/example_battery
Command line:
  gmx mdrun -v -s topol.tpr -deffnm constz


-------------------------------------------------------
Program:     gmx mdrun, version 2023
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -s
    File 'topol.tpr' 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 grompp, 2023 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/example_battery
Command line:
  gmx grompp -f /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/input/constant_area.mdp -c constz.gro -p system.top


-------------------------------------------------------
Program:     gmx grompp, version 2023
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
    File
    '/Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/input/constant_area.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 'constz.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, 2023 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /Users/ruben/Research/Projects/Ion_Batteries/polyply_regression_tests/examples/battery/example_battery
Command line:
  gmx mdrun -v -s topol.tpr -deffnm const_area


-------------------------------------------------------
Program:     gmx mdrun, version 2023
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -s
    File 'topol.tpr' 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
-------------------------------------------------------

[fgrunewald]

@rdguerrerom the error is right in the top of the script. Apparently it cannot find the bash function 'find_path', which means as a consequence it cannot find the input files for polyply that live in the tutorial files directory. Did you install the repository ? To make use of these functions you should run pip install ./ in the top-level of the repository. Otherwise you need to set the paths in the bash script by hand. Let me know how it goes and I can assist with further issues.

[rdguerrerom]

Thank you for your prompt response. Unfortunately, even after following your installation instructions for the repository, the error still persists.

I would be grateful if you could offer me additional assistance to resolve the issue.

[fgrunewald]

sorry to hear that it didn't work out. Could you tell me the operating system your using, the shell, as well as python version and if you installed the package into the conda environment. Basically the package should have installed the find_path command, which it didn't. That has to do either with the setup or your machine or a bug in the installation. Hence my questions

[rdguerrerom]

Thanks a lot for our guidance @fgrunewald.

My operating system is macOS Monterey 12.5.1. I am using bash and Python 3.9.7 (default, Sep 16 2021, 08:50:36). I am not using a conda environment, but rather installing everything in my local python.

Please let me know if there is anything else I can do.

[fgrunewald]

thanks! should be fixed now. There was a missing header in a script which causes some installation issues on Mac. Interestingly it is fine on Linux. If you update and reinstall, it should work.

[rdguerrerom]

It worked!

Thanks a lot, @fgrunewald !