Momentum and Velocity Scaling Rules in Replica-Exchange Molecular Dynamics Simulations with Mass Manipulation

Abstract

The authors have recently presented the mass-scaling replica-exchange molecular dynamics (MSREMD) method [J. Chem. Phys. 141, 114111 (2014)], in which all masses are scaled in proportion to temperature for better numerical stability with a large time step. In addition, the scaling of masses, performed in advance of the simulation, can be substituted for the velocity scaling necessary after every accepted replica-exchange attempt, and the algorithm can thereby be simplified. In this work, the authors present the mass-manipulating REMD (MMREMD) method, where arbitrary mass scaling is employed. Rules for momentum and velocity scaling are formalized for the MMREMD method, followed by a demonstration with two replicas. Adherence to these rules is crucial for sampling of the correct canonical distribution. The authors also review and discuss a previous study as a sample application of the MMREMD method.