Multi-replica molecular dynamics modeling

Abstract

We propose a new unified modeling concept, multi-replica molecular dynamics (MRMD), which is a collective designation for molecular dynamics (MD) or particle dynamics (PD) that simultaneously follows the time evolution of two or more replica systems. Numerous methods in various fields (physics, chemistry, biology, materials science, astronomy, etc.) can be classified in MRMD, such as parallel replica methods, the nudged elastic band method, path integral methods, replica exchange methods, and the multi-walker metadynamics method. However, the relations between these MRMD methods have not been clarified, and a global understanding or unified methodological framework remains to be presented. Therefore, herein, we discuss the relations between various MRMD methods to provide a comprehensive understanding of these methods. Then, with this understanding, we describe a concise implementation of MRMD into conventional domain- and particle-decomposition parallel MD program codes, instead of the somewhat intuitive replica-parallel implementation. Finally, we demonstrate examples of different MRMD calculations performed using our parallel MRMD program “ParaMrMD.”