Derivation and testing of explicit equations of motion for polymers described by internal coordinates

Abstract

General Lagrange's equations of motion for a system of polymeric molecules are obtained in an explicit form. They can be used for simulating molecular dynamics of large molecules. The molecular conformations are described by internal coordinates, i.e., bond lengths, valence angles, and torsion angles. The equations derived permit any internal degrees of freedom to be frozen. The method is applied to an oligopeptide in an α-helical conformation. Three models of the molecule with different degrees of fixation are compared. It is shown that the method permits one to increase significantly the time step in molecular dynamics calculations.