Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function.

A symplectic multiple-time-step (MTS) algorithm has been developed for the united-residue (UNRES) force field. In this algorithm, the slow-varying forces (which contain most of the long-range interactions and are, therefore, expensive to compute) are integrated with a larger time step, termed the basic time step, and the fast-varying forces are integrated with a shorter time step, which is an integral fraction of the basic time step. Based on the split operator formalism, the equations of motion were derived. Separation of the fast- and slow-varying forces leads to stable molecular dynamics with longer time steps. The algorithms were tested with the Ala10 polypeptide chain and two versions of the UNRES force field: the current one in which the energy components accounting for the energetics of side-chain rotamers (Urot) can lead to numerically unstable forces and a modified one in which the the present Urot was replaced by a numerically stable expression which, at present, is parametrized only for polyala...