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 αhelical 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.
 Publication:

Journal of Computational Physics
 Pub Date:
 February 1991
 DOI:
 10.1016/00219991(91)90210C
 Bibcode:
 1991JCoPh..92..261M