New equations of motion for molecular dynamics systems that change shape

Abstract

In the methods of molecular dynamics a large system is frequently subdivided into smaller regions which are periodic replications of each other. This subdivision defines the ‘‘computational cell’’ and may be performed in a number of equivalent ways, all producing cells of different shapes but of the same size and containing equivalent sets of particles. We consider the requirement that the form of the equations of motion be invariant under transformations connecting such equivalent computational cells. Since none of the equations of motion of the Parrinello–Rahman family proposed so far satisfy this condition, we construct some which do. These new equations are more practically useful than their antecedents for studies of systems whose computational cells may undergo extensive changes in shape, especially for studies of yield and flow under an applied stress.