********** User guide ********** .. highlight:: bash This guide provides * material introducing |Gromacs| * practical advice for making effective use of |Gromacs|. For getting, building and installing |Gromacs|, see the :doc:`/install-guide/index`. For background on algorithms and implementations, see the `reference manual`_. .. _reference manual: gmx-manual-parent-dir_ .. TODO This is going to require more organization now that we are getting more content available. .. toctree:: :maxdepth: 2 getting-started system-preparation managing-simulations faq force-fields cutoff-schemes cmdline mdp-options mdrun-features mdrun-performance run-time-errors file-formats terminology environment-variables floating-point