A Simple Overview for Proteins Molecular Dynamics Simulations Using GROMACS

Molecular dynamics (MD) simulation is a computational technique capable of studying protein movements at the atomic scale and over a long-time scale. GROMACS is a free and powerful software used for protein MD simulations. The aim of this paper is to describe the different steps required for performing protein MD simulations using GROMACS. We explain first how proteins three dimensional (3D) structures are generated and how one could generate them if they are not available. We describe second the different steps required for protein MD simulation ranging from preparation of protein 3D structure, preparing the protein for MD simulation, MD production, and analysis of results.