Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

ABSTRACT: Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress

SUBMITTER: Gallicchio E 

PROVIDER: S-EPMC4834714 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature