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https://github.com/becksteinlab/gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
https://github.com/becksteinlab/gromacswrapper

gromacs gromacswrapper molecular-dynamics python science

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GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

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README 

        
.. -*- mode: rst, coding: utf-8 -*-

.. The whole GromacsWrapper package is Copyright (c) 2009-2018 Oliver

.. Beckstein and AUTHORS except where noted otherwise.



========================

 README: GromacsWrapper

========================



|build| |cov| |docs| |zenodo| |black| |PRsWelcome| |anaconda|



A primitive Python wrapper around the Gromacs_ tools. The library is

tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, 2021.x, 2022.x,

2023.x, 2024.x (and 5.x and 2016.x should also work). It supports

Python 3.9--3.12 on Linux and macOS.



GromacsWrapper also provides a small library (cook book) of often-used

recipes and helper functions to set up MD simulations.



`Documentation`_ is mostly provided through the python doc strings and

available at https://gromacswrapper.readthedocs.org for recent releases.



The source code is available in the `GromacsWrapper git repository`_.



Please be aware that this software is only minimally maintained and it

most definitely contains bugs. It is *your* responsibility to ensure

that you are running simulations with sensible parameters.



.. _Gromacs: http://www.gromacs.org

.. _Documentation: 

   https://gromacswrapper.readthedocs.org/en/latest/

.. _GromacsWrapper git repository:

   https://github.com/Becksteinlab/GromacsWrapper

.. |build| image:: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml/badge.svg?branch=main

   :target: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml

   :alt: Build Status	     

.. |cov| image:: https://codecov.io/gh/Becksteinlab/GromacsWrapper/graph/badge.svg?token=LvbLZ49wxN

   :target: https://codecov.io/gh/Becksteinlab/GromacsWrapper

   :alt: Code Coverage

.. |zenodo| image:: https://zenodo.org/badge/13219/Becksteinlab/GromacsWrapper.svg

   :target: https://zenodo.org/badge/latestdoi/13219/Becksteinlab/GromacsWrapper

   :alt: Latest release on zenodo (with DOI)

.. |docs| image:: https://readthedocs.org/projects/gromacswrapper/badge/?version=latest

   :target: https://gromacswrapper.readthedocs.org/en/latest/?badge=latest

   :alt: Documentation

.. |PRsWelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg

   :target: http://makeapullrequest.com

   :alt: PRs Welcome!	 

.. |anaconda| image:: https://anaconda.org/conda-forge/gromacswrapper/badges/version.svg

   :target: https://anaconda.org/conda-forge/gromacswrapper

   :alt: Anaconda.org package

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg

   :target: https://github.com/psf/black	 

   :alt: black   



	 

	 

Quick Start

===========



Given a PDB file ``1iee.pdb``, set up and run a simple simulation (assuming

you have all other input files at hand such as the MDP files)::



  >>> import gromacs

  >>> print(gromacs.release)

  2018.2

  >>> help(gromacs.pdb2gmx)

  DESCRIPTION



  gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files,

  adds hydrogens to the molecules and generates coordinates in GROMACS

  ...

  ...

  OPTIONS



  Options to specify input files:



  -f      [<.gro/.g96/...>]  (eiwit.pdb)

            Structure file: gro g96 pdb brk ent esp tpr

  ...

  ...

  >>> gromacs.pdb2gmx(f="1iee.pdb", o="protein.gro", p="topol.top",

  ...                 ff="oplsaa", water="tip4p")

  >>> gromacs.editconf(f="protein.gro", o="boxed.gro",

  ...                  bt="dodecahedron", d=1.5, princ=True,

  ...                  input="Protein")

  >>> gromacs.solvate(cp="boxed.gro", cs="tip4p", p="topol.top",

  ...                 o="solvated.gro")

  >>> gromacs.grompp(f="emin.mdp", c="solvated.gro", p="topol.top",

  ...                o="emin.tpr")

  >>> gromacs.mdrun(v=True, deffnm="emin")

  >>> gromacs.grompp(f="md.mdp", c="emin.gro", p="topol.top", o="md.tpr")

  >>> gromacs.mdrun(v=True, deffnm="md")



	 

License

=======



The **GromacsWrapper** package is made available under the terms of

the `GNU Public License v3`_ (or any higher version at your choice)

except as noted below. See the file COPYING for the licensing terms

for all modules.



.. _GNU Public License v3: http://www.gnu.org/licenses/gpl.html



Installation

============



Releases

--------



The `latest version of GromacsWrapper from PyPi`_ can be installed

with ::



  pip install GromacsWrapper



or as a `conda-forge package`_ with ``conda`` from the *conda-forge* channel ::



   conda install -c conda-forge gromacswrapper

    



.. _`latest version of GromacsWrapper from PyPi`:

   https://pypi.org/project/GromacsWrapper/



.. _`conda-forge package`:

   https://anaconda.org/conda-forge/gromacswrapper



Development version

-------------------



The *main* branch in the GitHub source repository generally

contains useful code but nevertheless, things can break in weird and

wonderful ways. Please report issues through the `Issue Tracker`_.



To use the *development code base*:  checkout the ``main`` branch::



   git clone https://github.com/Becksteinlab/GromacsWrapper.git   



and install ::



   pip install GromacsWrapper/



Code contributions are welcome. We use `black`_ for uniform code

formatting so please install black_ and run it on your code.



.. _`black`: https://github.com/psf/black



Download and Availability

=========================



The GromacsWrapper home page is

http://github.com/Becksteinlab/GromacsWrapper.  The latest release of the

package is being made available from https://github.com/Becksteinlab/GromacsWrapper/releases



You can also clone the `GromacsWrapper git repository`_ or fork for

your own development::



  git clone git://github.com/Becksteinlab/GromacsWrapper.git



Questions

=========



Please ask questions in the `Discussion forum`_ (instead of private email).



Reporting Bugs and Contributing to GromacsWrapper

=================================================



Please use the `Issue Tracker`_ to report bugs, installation problems,

and feature requests. Ask questions in the `Discussion forum`_.



**Pull requests** for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a 

general introduction on how make a pull request and contribute to open source projects.



.. _Issue Tracker: https://github.com/Becksteinlab/GromacsWrapper/issues

.. _Discussion forum: https://github.com/Becksteinlab/GromacsWrapper/discussions



Building Documentation

======================



Install Sphinx::



   pip install sphinx



and compile::



  cd GromacsWrapper

  python setup.py build_sphinx

  



Citing

======



|zenodo|



GromacsWrapper was written by Oliver Beckstein with contributions from

many other people. Please see the file AUTHORS_ for all the names.



If you find this package useful and use it in published work I'd be

grateful if it was acknowledged in text as



  "... used GromacsWrapper (Oliver Beckstein et al,

  https://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)"



or in the Acknowledgements section.



Thank you.



.. _AUTHORS:

   https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/main/AUTHORS