Molecular simulation is a type of N-body simulation technique used for studying the physical movements of atoms and molecules. In molecular simulations, the dynamics of the system are simulated by allowing the atoms and molecules to interact for a fixed period of time. The forces between the interacting atoms or molecules and their potential energies are calculated using interparticle potentials or molecular mechanics force fields. In molecular dynamics simulations, Newton's equations of motion are solved numerically to generate a series of snapshots of the simulated system, thus providing trajectories of the atoms and molecules.
Image credit: Vlad Cojocaru (MPI for Molecular Biomedicine, Münster, Germany), see also: Cojocaru et al. Structure and Dynamics of the Membrane Bound Cytochrome P450 2C9. PLoS Comput. Biol., (2011) 7(8):e1002152.