title: Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.
abstract: Replica-exchange molecular dynamics (REMD) is a popular sampling method in the molecular simulation. By frequently exchanging the replicas at different temperatures, the molecule can jump out of the minima and sample efficiently in the conformational space. Although REMD has been shown to be practical in a lot of applications, it does have a critical limitation. All the replicas at all the temperatures must be simulated for a period between the replica-exchange steps. This may be problematic for the reaction with high free energy barriers. In that case, too many replicas are required in the simulation. To reduce the calculation quantity and improve its performance, in this paper we propose a modified REMD method. During the simulation, each replica at each temperature can stay in either the active or inactive state and only switch between the states at the exchange step. In the active state, the replica moves freely in the canonical ensemble by the normal molecular dynamics, and in the inactive state, the replica is frozen temporarily until the next exchange step. The number of the replicas in the active states (active replicas) depends on the number of CPUs in the computer. Using the additional inactive replicas, one can perform an REMD simulation in a wider temperature space. The practical applications show that the modified REMD method is reliable. With the same number of active replicas, this REMD method can produce a more reasonable free energy surface around the free energy minima than the standard REMD method.
authors.affiliation: Biomolecular Physics and Modelling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
authors.forename: Changjun
authors.initials: C
authors.lastname: Chen
authors.affiliation: Biomolecular Physics and Modelling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: Biomolecular Physics and Modelling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
authors.forename: Yanzhao
authors.initials: Y
authors.lastname: Huang
mesh_terms: D004151:Dipeptides / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry; D011789:Quantum Theory; D013696:Temperature
chemical_list: D004151:Dipeptides; D011506:Proteins; C539234:Trpzip2 protein; C002956:alanylalanine