Paper Info
Title
Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis
Abstract
We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta-cyclodextrin-heptanoate host-guest system in the context of one- and two-dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (>picoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle. (c) 2015 Wiley Periodicals, Inc.
Year
DOI
Venue
2015
10.1002/jcc.23996
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
DocType
Volume
asynchronous replica exchange,molecular dynamics,distributed computing network,efficiency analysis,binding energy distribution analysis method,host-guest system
Journal
36
Issue
ISSN
Citations 
23
0192-8651
5
PageRank 
References 
Authors
0.52
13
7
Name
Order
Citations
PageRank
Junchao Xia1162.74
William F. Flynn2163.08
Emilio Gallicchio319324.66
Bin W. Zhang450.85
Peng He5242.31
Zhiqiang Tan681.59
Ronald M Levy727132.01