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

Cython
NumPy

Gromacs installation

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.

Manual setup

The shared library of GROMACS 5.1and the corresponding c++ header files need to be present on the system. If the shared library is installed globally, the environment variable LD_LIBRARY_PATH must be set. The installation process will look for the header files by replacing any lib folder in LD_LIBRARY_PATH with include.

If no header files are present, simply pull the submodule gromacs in this repository. To build the shared library, follow the official installation instructions, starting with step 4 (creating a build directory).

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.

Deploy on intranet

For any installed version of mdevaluate modules do:

version=dev # or maybe: version=$(python ../mdevaluate/setup.py --version)
module load gromacs/5.1
module load mdevaluate/$version
python setup.py install --prefix=/autohome/niels/modules/mdevaluate-$version