Paper Citing NAMD - Abstract
Miyashita, Naoyuki; Re, Suyong; Sugita, Yuji
REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115:325-332, MAR 5 2015
Replica-exchange molecular dynamics (REMD) method is one of the enhanced conformational sampling algorithms widely applied in computational biophysics and biochemistry. In the method, molecular dynamics (MD) simulations for multiple replicas of a target system are performed simultaneously and independently. Every few steps, temperatures or other parameters are exchanged between a pair of replicas according to the modified Metropolis criteria. Replica-Exchange INterface (REIN) is interface software for REMD simulations. It utilizes existing MD software without modification and performs the exchanges of replicas. In this article, we introduce the software design of REIN and demonstrate its applicability through benchmark simulations of alanine pentapeptide in explicit water, as well as the free-energy analysis of N-glycan and Tom20-presequence complex in solution. (c) 2014 Wiley Periodicals, Inc.
