Special geometrical constraints in the molecular dynamics of chain molecules

Abstract

The molecular dynamics simulation of chain molecules with a full atomic description is considered in the particular case of a n-alkane molecule. In order (a) to keep the time step in the numerical integration of the equations of motions to a reasonable value (10-15-10-14s) and (b) to describe such flexible systems with a minimum number of degrees of freedom, it is useful to impose geometrical constraints in order to freeze the fastest intramolecular motions of the chain. Given the large number and the nature of the geometrical constraints involved in this model, the method of constraints used to solve the dynamics in terms of atomic cartesian coordinates needs to be generalized to arbitrary constraints and solved in an iterative way. Such a method is proposed and illustrated on a ring alkane chain, namely cyclo-tetradecane (C14H28).