.. |organization| replace:: scipion-chem
.. |repository| replace:: scipion-chem-gromacs
   
.. _docs-chem-gromacs:

.. figure:: ../../../_static/images/plugins/gromacs/logo.png
   :alt: gromacs logo

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scipion-chem-gromacs
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`Gromacs <https://www.gromacs.org/>`_ is a free and open-source software suite for high-performance Molecular
Dynamics (MD) and output analysis. In Scipion-chem-gromacs, we have integrated tools for preparing MD systems,
running simulations and modifying and analyzing the output trajectories.

==========================================
Installation
==========================================
A) Requirements
~~~~~~~~~~~~~~~~~~~~~~~~~~~
In order to use this plugin, you need to install first :ref:`pwchem-index`.

B) Installation steps
~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. include:: ../../templates/plugins/installation/installation-steps.rst
.. include:: ../../templates/plugins/installation/only-devel.rst

==========================================
Protocols
==========================================

- :ref:`gromacs-system-preparation`: Prepares a Gromacs MD system prior to its simulation from a ``AtomStruct`` object.
- :ref:`gromacs-md-simulation`: Takes the prepared Gromacs system and use it to run a defined simulation.
- :ref:`gromacs-system-modification`: Performs `modifications <https://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-trjconv.html>`_ over a Gromacs System, specially over its trajectory.