Atomic motions are responsible for the molecular properties, be it a small molecule like carbon di-oxide or a large molecule like proteins. Molecular dynamics simulations with the advent of faster computers emerge an indispensable tool to understand the condensed phase properties. In this lecture we shall learn how to use Molecular Dynamics methods to describe the atomic motions in a protein and relate to its function to conformation. We also apply computer simulations to study structural changes in non-equilibrium steady state conditions  achieved by creating temperature difference where the particle sizes  are sensitive to temperature.