Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 30, Issue 11, Pages 1719-1725Publisher
WILEY-BLACKWELL
DOI: 10.1002/jcc.21285
Keywords
molecular dynamics simulation; replica exchange; enhanced sampling; free energy; thermodynamics
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Funding
- Howard Hughes Medical Institute Funding Source: Medline
- NCRR NIH HHS [P 41 RR08605] Funding Source: Medline
- NIGMS NIH HHS [R01 GM031749-27, GM31749, R01 GM031749] Funding Source: Medline
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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. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 1719-1725, 2009
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