Why do we perform MD simulations?

• In order to predict the properties of a molecular substance (from Frenkel and Smit., chapter 1).

  Molecular simulations done using a computer help predict molecular properties of a substance. Prior to simulations, the only other method to do this was to make use of a theory that provided an approximate description of the material.

• Many experimentalists use MD simulations as a tool to analyze or interpret their measurements whenever the system becomes significantly complex. (M.A.Gonzalez)

  This was observed in the case of neutron scattering, when experimental observables correlate directly with properties deduced from MD simulations.

• MD simulations can be used to study protein dynamics and function and understand how they bind with small molecules or other proteins. (Outi M. H. Salo-Ahen)

  Drug discovery processes often start with identifying and validating a biologically relevant target (often different kinds of proteins) that can be modulated with drug molecules to prevent or cure a disease or alleviate symptoms of sickness. MD simulations can provide important information on the dynamic character of the target with regard to drug design.