title: Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method.
abstract: Replica Exchange Molecular Dynamics (REMD) method is a powerful sampling tool in molecular simulations. Recently, we made a modification to the standard REMD method. It places some inactive replicas at different temperatures as well as the active replicas. The method completely decouples the number of the active replicas and the number of the temperature levels. In this article, we make a further modification to our previous method. It uses the inactive replicas in a different way. The inactive replicas first sample in their own knowledge-based energy databases and then participate in the replica exchange operations in the REMD simulation. In fact, this method is a hybrid between the standard REMD method and the simulated tempering method. Using different active replicas, one can freely control the calculation quantity and the convergence speed of the simulation. To illustrate the performance of the method, we apply it to some small models. The distribution functions of the replicas in the energy space and temperature space show that the modified REMD method in this work can let the replicas walk freely in both of the two spaces. With the same number of the active replicas, the free energy surface in the simulation converges faster than the standard REMD. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Biomolecular Physics and Modelling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, 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, Hubei, 430074, China.
authors.forename: Yanzhao
authors.initials: Y
authors.lastname: Huang
keywords: Monte Carlo; free energy calculation; molecular dynamics; replica exchange molecular dynamics