Premium
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics
Author(s) -
Fajer Mikolai,
Swift Robert V.,
McCammon J. Andrew
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21285
Subject(s) - replica , histogram , molecular dynamics , statistical physics , pairwise comparison , observable , scaling , computer science , exponential function , energy (signal processing) , algorithm , chemistry , physics , computational chemistry , mathematics , quantum mechanics , artificial intelligence , art , mathematical analysis , image (mathematics) , geometry , visual arts
Replica exchange accelerated molecular dynamics (REXAMD) is a method that enhances conformational sampling while retaining at least one replica on the original potential, thus avoiding the statistical problems of exponential reweighting. In this article, we study three methods that can combine the data from the accelerated replicas to enhance the estimate of properties on the original potential: weighted histogram analysis method (WHAM), pairwise multistate Bennett acceptance ratio (PBAR), and multistate Bennett acceptance ratio (MBAR). We show that the method that makes the most efficient use of equilibrium data from REXAMD simulations is the MBAR method. This observation holds for both alchemical free energy and structural observable prediction. The combination of REXAMD and MBAR should allow for more efficient scaling of the REXAMD method to larger biopolymer systems. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009