Pygmx

A Cython wrapper for the shared library of GROMACS 2018

Installation

Pygmx requires some python packages and an installation of GROMACS 2018.

Python requirements

Pygmx needs mainly two python packages to be installed, which are available in any major Python distribution.

• Cython
• NumPy

Gromacs installation

Pygmx requires the shared library and header files of GROMACS 2018 to be installed.

Example install scripts are provided. For Debian 12 a patch file is included to be able to compile GROMACS 2018.8.

Through package manager

On many Unix distributions, Gromacs may be installed through the package manager. The required packages, which provide the headers, are usually named gromacs-devel or gromcas-dev.

Manual build

To build the shared library manually, follow the official installation instructions. Make sure to source the GMXRC script, which sets the environment variable LD_LIBRARY_PATH to the correct location or set this variable manually. Don't bother with advanced features like GPU support if the Gromacs installation will only be used for pygmx, since the file io functions do not use these features.

Installing pygmx

When the requirements are met, installing pygmx into the local Python installation can be achieved by navigating to the top folder of the repository and running the command

pip3 install -r requirements.txt
pip install .

This builds the cython modules and installs them into the local python distribution. To check if everyting works, run the following command from a directory outside of the repository

python -c 'import pygmx'

If this raises an error that refers to libgromacs.so, the Gromacs library could not be found. Make sure it is either in a standard location or LD_LIBRARY_PATH is set correctly.