GromacsWrapper — a Python framework for Gromacs¶
July 23, 2021
GromacsWrapper is a Python package (Python 2.7.x and Python ≥ 3.6) that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into Python scripts. This is generally superior to shell scripts because of Python’s better error handling and superior data structures. It also allows for modularization and code re-use. In addition, commands, warnings and errors are logged to a file so that there exists a complete history of what has been done.
Gromacs versions 4.6.x, 2016.x, 2018.x, 2019.x, 2020.x, and 2021.x are all
supported. GromacsWrapper detects your Gromacs tools and provides them
gromacs.mdrun(), etc, regardless of
your Gromacs version, which allows one to write scripts that are
broadly Gromacs-version agnostic. Source your
GMXRC file or make
the gmx binary (for versions ≥ 5.x) or all the Gromacs
tools available on your
PATH for GromacsWrapper to find the
Although GromacsWrapper has been used in published research over the last 10 years or so, there is no guarantee that any of the defaults chosen are suitable for any particular project or simulation setup.
It is your responsibility to ensure that you are running simulations with sensible parameters. Provide appropriate template files instead of the bundled defaults and check the logger output!
Any feedback, bug reports, suggestions and contributions are very welcome.
Other approaches to interfacing Python and Gromacs are listed under Alternatives to GromacsWrapper.
See Installation for download and installation instructions. The Quick Start provides a brief example of how to use GromacsWrapper in the most basic fashion.
The source code itself is available in the GromacsWrapper git repository.
You also need to have a version of Gromacs installed.
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.
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.
Please use the Issue Tracker to report bugs, installation problems,
and feature requests (mention
@orbeckst in the issue report).