An alternative derivation of the equations of motion in torsion space for a branched linear chain

Abstract

Torsion space molecular dynamics may be more efficiently encoded if the global motions are separated from the internal motions. The equations of motion for single, noncyclic chains are shown to be first order in the backbone angle parameters when the global frame of reference is ignored and second order otherwise. Adding a simple heuristic substitute for the global motions enables the encoding of dynamics for mixed constrained/unconstrained model systems.