.. _reference manual: gmx-manual-parent-dir_ .. _gmx-beginners: Beginners --------- For those just starting out with |Gromacs| and / or :ref:`Molecular Dynamics Simulations ` it can be very daunting. It is highly recommended that the various and extensive documentation that has been made available for |Gromacs| is read first, plus papers published in the area of interest. Resources ^^^^^^^^^ * |Gromacs| :doc:`/reference-manual/index/` - very detailed document that can also act as a very good introduction for :ref:`MD ` in general. * :doc:`Flow Chart `- simple flow chart of a typical |Gromacs| MD run of a protein in a box of water. * Molecular dynamics simulations and |Gromacs| introduction (`slides `_, `video `_) - force fields, integrators, control of temperature and pressure (Berk Hess).