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Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software.

Project description Documentation Status


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.

Quick install

The latest release can be installed via pip or 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


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


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

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