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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.

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

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.

Main features:

  • Python Scriptable simulation:

    • Topologie creation

    • Solvation

    • Ion insertion

    • Energy minimisation

    • Equilibration with different position restraints

    • Production

  • Topologie manipulation starting from a raw PDB:

    • Amino acid protonation and pKa calculation using apbs/pdb2pqr

    • Position constraints file .itp creation

    • Cyclic peptide topologie

    • Cystein bond topologie modification

    • ligand topologie using ambertools and acpype

  • Advanced simulation tools:

    • Monitor a simulation while running

    • Free Energy calculations

    • Interrupt a simulation if a criterion is met (Not implemented yet)

Compatibility

  • Supported Gromacs versions:

    • 2020

    • 2019*

    • 2018*

    • 2017

    • 2016

    • 5.1

    • 5.0

  • Supported Python versions:

    • 3.8*

    • 3.7*

    • 3.6*

  • Supported OS:

    • osx*

    • linux*

* tested after each code submission.

Indices and tables