Asynchronous replica exchange for molecular simulations

Emilio Gallicchio; Ronald M. Levy; Manish Parashar

doi:10.1002/jcc.20839

journal article Sep 17, 2007

Asynchronous replica exchange for molecular simulations

Emilio Gallicchio

Ronald M. Levy

Manish Parashar

Journal of Computational Chemistry Vol. 29 No. 5 pp. 788-794 · Wiley

View at Publisher Save 10.1002/jcc.20839

Abstract

AbstractAn 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. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

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Metrics

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Citations

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References

Details

Published: Sep 17, 2007
Vol/Issue: 29(5)
Pages: 788-794
License: View

Authors

E

Emilio Gallicchio

City University of New York

Cornell University

Cite This Article

Emilio Gallicchio, Ronald M. Levy, Manish Parashar (2007). Asynchronous replica exchange for molecular simulations. Journal of Computational Chemistry, 29(5), 788-794. https://doi.org/10.1002/jcc.20839

Asynchronous replica exchange for molecular simulations

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