Mechanical Constraints in Molecular Dynamics Simulation

Advances in computational power and algorithm development have stimulated molecular dynamics research on diverse large and complicated physical systems. Part of this progress relies on algorithms that are able to account for widely separated time scales or activated processes that would otherwise degrade computational efficiency. This chapter describes how holonomic constraints can be used to overcome such difficulties. The constrained dynamical equations, the statistical mechanics that follows from these equations, and the algorithms needed to simulate the dynamics are presented. Examples related to rare event sampling and adiabatic dynamics are given to illustrate the methods.