GromacsWrapper — a Python framework for Gromacs¶
July 21, 2020
GromacsWrapper is a Python package (Python 2.7.x and Python > 3.4) 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, and 2019.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 ≥ 2016) or all the gromacs
tools available on your
PATH for GromacsWrapper to find the
See INSTALL 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.
Please be aware that this is beta software that most definitely contains bugs. The API is not stable yet and can change between releases.
It is your responsibility to ensure that you are running simulations with sensible parameters.
The package and the documentation are still in flux and any feedback, bug reports, suggestions and contributions are very welcome. See the package README: GromacsWrapper for contact details.
Other approaches to interfacing Python and Gromacs are listed under Alternatives to GromacsWrapper.
- Quick Start
- GromacsWrapper package
- Alternatives to GromacsWrapper