Introduction to a Molecular Dynamics Simulation

Abstract

In this chapter a summary is given of the key ingredients necessary to carry out a molecular dynamics simulation, with particular emphasis on macromolecular systems. We discuss the form of the intermolecular potential for molecules composed of atoms, and of non-spherical sub-units, giving examples of how to compute the forces and torques. We also describe some of the MD algorithms in current use. Finally, we briey refer to the factors that inuence the size of systems, and length of runs, that are needed to calculate statistical properties.