sscake / gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2021 supported).

README: GromacsWrapper

A primitive Python wrapper around the Gromacs tools. The library is tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, and 2021.x (and 5.x and 2016.x should also work). It supports Python 2.7 and 3.6--3.9 on Linux and macOS.

GromacsWrapper also provides a small library (cook book) of often-used recipes and helper functions to set up MD simulations.

Documentation is mostly provided through the python doc strings and available at https://gromacswrapper.readthedocs.org for recent releases.

The source code is available in the GromacsWrapper git repository.

Please be aware that this is beta software that most definitely contains bugs. It is your responsibility to ensure that you are running simulations with sensible parameters.

Quick Start

Given a PDB file 1iee.pdb, set up and run a simple simulation (assuming you have all other input files at hand such as the MDP files):

>>> import gromacs
>>> print(gromacs.release)
2018.2
>>> help(gromacs.pdb2gmx)
DESCRIPTION

gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files,
adds hydrogens to the molecules and generates coordinates in GROMACS
...
...
OPTIONS

Options to specify input files:

-f      [<.gro/.g96/...>]  (eiwit.pdb)
          Structure file: gro g96 pdb brk ent esp tpr
...
...
>>> gromacs.pdb2gmx(f="1iee.pdb", o="protein.gro", p="topol.top",
...                 ff="oplsaa", water="tip4p")
>>> gromacs.editconf(f="protein.gro", o="boxed.gro",
...                  bt="dodecahedron", d=1.5, princ=True,
...                  input="Protein")
>>> gromacs.solvate(cp="boxed.gro", cs="tip4p", p="topol.top",
...                 o="solvated.gro")
>>> gromacs.grompp(f="emin.mdp", c="solvated.gro", p="topol.top",
...                o="emin.tpr")
>>> gromacs.mdrun(v=True, deffnm="emin")
>>> gromacs.grompp(f="md.mdp", c="emin.gro", p="topol.top", o="md.tpr")
>>> gromacs.mdrun(v=True, deffnm="md")

License

The GromacsWrapper package is made available under the terms of the GNU Public License v3 (or any higher version at your choice) except as noted below. See the file COPYING for the licensing terms for all modules.

Installation

Releases

The latest version of GromacsWrapper from PyPi can be installed with

pip install GromacsWrapper

or as a bioconda package with conda from the bioconda channel

conda install -c conda-forge -c bioconda gromacswrapper

Development version

The master branch in the GitHub source repository generally contains useful code but nevertheless, things can break in weird and wonderful ways. Please report issues through the Issue Tracker and mention that you used the develop branch.

To use the development code base: checkout the master branch:

git clone https://github.com/Becksteinlab/GromacsWrapper.git
cd GromacsWrapper

and install

python setup.py install

Download and Availability

The GromacsWrapper home page is http://github.com/Becksteinlab/GromacsWrapper. The latest release of the package is being made available from https://github.com/Becksteinlab/GromacsWrapper/releases

You can also clone the GromacsWrapper git repository or fork for your own development:

git clone git://github.com/Becksteinlab/GromacsWrapper.git

Questions

Please ask questions in the Issue Tracker (instead of private email).

Reporting Bugs and Contributing to GromacsWrapper

Please use the Issue Tracker to report bugs, installation problems, and feature requests.

Pull requests for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a general introduction on how make a pull request and contribute to open source projects.

Building Documentation

Install Sphinx:

pip install sphinx

and compile:

cd GromacsWrapper
python setup.py build_sphinx

Citing

GromacsWrapper was written by Oliver Beckstein with contributions from many other people. Please see the file AUTHORS for all the names.

If you find this package useful and use it in published work I'd be grateful if it was acknowledged in text as

"... used GromacsWrapper (Oliver Beckstein et al, https://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)"

or in the Acknowledgements section.

Thank you.