Chapter 4 - Molecular Dynamics Simulations

Abstract

Molecular Dynamics (MD) simulations are in many respects very similar to real experiments. In MD, first, sample is prepared, a model system consisting of N particles is selected, and then Newton's equations of motion are solved for the system until the properties of the system no longer change with time. To measure an observable quantity in a MD simulation, one must first of all be able to express this observable as a function of the positions and momenta of the particles in the system. The best introduction to MD simulations is to consider a simple program. To start the simulation, one should assign initial positions and velocities to all particles in the system. The particle positions should be chosen compatible with the structure that one is aiming to simulate. A good MD program requires a good algorithm to integrate Newton's equations of motion. Accuracy for large time steps is more important because the longer the time step that one can use, the fewer evaluations of the forces are needed per unit of simulation time. For most MD applications, Verlet-like algorithms are perfectly adequate. However, sometimes it is convenient to employ a higher-order algorithm.