.. _gmx-reference-manual-rst:

****************
Reference Manual
****************

.. highlight:: bash

.. TODO this needs to be carefully checked that I didn't mess anything up too bad

This part of the documentation covers implementation details of |Gromacs|.

For quick simulation set-up and short explanations,
please refer to the :ref:`User guide <user guide>`.

Help with the installation of |Gromacs| can be found in the
:ref:`Install guide <install guide>`.

If you want to help with developing |Gromacs|, your are most welcome
to read up on the :ref:`Developer Guide <dev guide>` and continue
right away with coding for |Gromacs|.

.. toctree::
   :maxdepth: 2
   
   preface
   introduction
   definitions
   algorithms
   functions
   topologies
   file-formats
   special
   run-parameters
   analysis
   details
   averages
   references