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) s

SUBMITTER: Xia J 

PROVIDER: S-EPMC4512903 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature