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Large‐Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis
Author(s) -
Xia Junchao,
Flynn William F.,
Gallicchio Emilio,
Zhang Bin W.,
He Peng,
Tan Zhiqiang,
Levy Ronald M.
Publication year - 2016
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.24336
Subject(s) - computer science , replica , asynchronous communication , context (archaeology) , distributed computing , homogeneous , grid , grid computing , scale (ratio) , computational science , parallel computing , theoretical computer science , statistical physics , computer network , physics , mathematics , paleontology , geometry , visual arts , art , quantum mechanics , biology
The ASyncRE methodology is presented, allowing the performance of large‐scale replica exchange molecular dynamics (REMD) simulations asynchronously on grid computing networks consisting of heterogeneous and distributed computing environments, as well as on homogeneous high performance clusters like NSF XSEDE clusters and BOINC distributed computing networks at Temple University and Brooklyn College at CUNY. Several ways to improve the efficiency of REMD simulations in the context of the ASyncRE methodology are also proposed.