:orphan: true

.. _gromacs-system-preparation:

###############################################################
Gromacs system preparation
###############################################################
This protocol prepares a Gromacs MD system prior to its simulation from a ``AtomStruct`` object. This protein must have all the atoms including hydrogens, we recommend you to prepare it first with any of our integrated protocols for receptor preparation.

It allows the user to create a solute boundary box, define the force field and finally specify the ions in the solute,
which can be set to neutralize the charges, or manually add the desired number.

.. note::
   Unfortunately, as for today we do not include the functionality for preparing complexes containing non-protein atoms,
   such as ligands. Hopefully it will be coming soon.

Input
----------------------------------------
.. include:: ../../../templates/plugins/input-help.rst

.. image:: ../../../../_static/images/plugins/gromacs/system-preparation/form_1.png
   :alt: Gromacs system preparation form 1
   :height: 400
   :align: center

|

.. image:: ../../../../_static/images/plugins/gromacs/system-preparation/form_2.png
   :alt: Gromacs system preparation form 2
   :height: 400
   :align: center

|

The result of this protocol is a ``GromacsSystem``, containing the Gromacs coordinates and topology files. The user
can visualize the complex with PyMol using **Analyze Results**.

.. image:: ../../../../_static/images/plugins/gromacs/system-preparation/output.png
   :alt: Gromacs system preparation form 2
   :height: 400
   :align: center

|

.. |testCommand| replace:: gromacs.tests.tests.TestGromacsPrepareSystem
.. include:: ../../../templates/plugins/protocol-test.rst