Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water

Abstract

Multicanonical molecular dynamics (McMD) simulation is an enhanced conformational sampling method. For more accelerated sampling, we examined a trajectory-parallelization method, which trivially integrates multiple McMD trajectories into one. This method decreases communications between computing nodes largely. We applied this method to conformational sampling of a seven-residue peptide in explicit water. Physical quantities converged well with those from a long McMD simulation in a wide temperature range. Thus, the integration can generate a canonical ensemble without performing the long simulation. The current method is useful for folding study of long polypeptides (proteins) in explicit water with massive parallelism.