.. _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 `. Help with the installation of |Gromacs| can be found in the :ref:`Install guide `. If you want to help with developing |Gromacs|, your are most welcome to read up on the :ref:`Developer 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 `. Help with the installation of |Gromacs| can be found in the :ref:`Install guide `. If you want to help with developing |Gromacs|, your are most welcome to read up on the :ref:`Developer Guide ` and continue right away with coding for |Gromacs|. .. toctree:: :maxdepth: 2 preface introduction definitions topologies file-formats run-parameters details averages references