.. _gmx-reference-manual-rst:

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

.. highlight:: bash

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

.. ifconfig:: gmx_image_convert == 'possible'

   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


.. ifconfig:: gmx_image_convert == 'impossible'

   The manual could not be properly build because we could not
   convert the images for proper display without Imagemagick.
   The rest of the documentation is still there, but this part here will be missing.

   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
      topologies
      file-formats
      run-parameters
      details
      averages
      references

