Pygmx
A Cython wrapper for the shared library of GROMACS 5.1.
Installation
Pygmx requires some python packages and an installation of GROMACS 5.1.
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 5.1 or higher to be installed.
Using a module
If gromacs is installed as a module in your system, run
module load gromacs/5.1
and skip to the section Installing pygmx.
Note that on the AG Vogel intranet pygmx is available through the module mdevaluate.
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, the installation should be easy. Navigate to the top folder of the repository and run the command
python setup.py install
This builds the cython modules and installs them into the local python distribution. To check if everyting works run
python -c 'import pygmx'
If this raises an error that refers to libgromacs.so, this means the Gromacs library could not be found.
Make sure it is either in a standard location or LD_LIBRARY_PATH is set correctly.