Gromacs_py

Gromacs_py is a Python library allowing a simplified use of the Gromacs MD simulation software. Gromacs_py can build a system topologie based on a pdb file, create the simulation system (pbc box, adding water and ions) and run minimisation, equilibration and production runs. One of the main objective of the Gromacs_py wrapper is to automatize routine operations for MD simulation of multiple systems.

Gromacs_py is under active development using continuous integration with Travis Cl.

• Online Documentation:

  https://gromacs-py.readthedocs.io

• Source code repository:

  https://github.com/samuelmurail/gromacs_py

Quick install

The latest release can be installed via pip or conda.

Conda

If you don't need a GPU compiled version of Gromacs you can use directly the Gromacs_py conda package to install both Gromacs software and Gromacs_py library:

conda install -c bioconda gromacs_py

Pip (Deprecated)

If the folowing softwares/modules are installed then you need to install the Gromacs_py library using pypi :

pip install gromacs_py

• Gromacs (version >= 5.1)
• Ambertools
• Rdkit
• Acpype

and add the software path Gromacs in the environmnent variable $PATH, eg. for gromacs:

# Add gromacs 'gmx' path:
export PATH='*path_to_gromacs*/bin/':$PATH

Authors

• Samuel Murail, Associate Professor - Université Paris Diderot, CMPLI.

See also the list of contributors who participated in this project.

License

This project is licensed under the GNU General Public License v2.0 - see the LICENSE file for details.