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J Comput Chem. 2008 Apr 15;29(5):788-94.

Asynchronous replica exchange for molecular simulations.

Author information

1
Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology Rutgers University, Piscataway, New Jersey 08854, USA. emilio@bionaps.rutgers.edu

Abstract

An asynchronous implementation of the replica exchange method that addresses some of the limitations of conventional synchronous replica exchange implementations is presented. In asynchronous replica exchange pairs of processors initiate and perform temperature replica exchanges independently from the other processors, thereby removing the need for processor synchronization found in conventional synchronous implementations. Illustrative calculations on a molecular system are presented that show that asynchronous replica exchange, contrary to the synchronous implementation, is able to utilize at nearly top efficiency loosely coupled pools of processors with heterogeneous speeds, such as those found in computational grids and CPU scavenging environments. It is also shown that employing non-nearest-neighbor temperature exchanges, which are straightforward to implement within the asynchronous algorithm, can lead to faster temperature equilibration across processors.

PMID:
17876761
PMCID:
PMC2977925
DOI:
10.1002/jcc.20839
[Indexed for MEDLINE]
Free PMC Article

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