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Journal of Molecular Modeling

, 21:243 | Cite as

Greedy replica exchange algorithm for heterogeneous computing grids

  • Christopher Lockhart
  • James O’Connor
  • Steven Armentrout
  • Dmitri K. Klimov
Original Paper

Abstract

Replica exchange molecular dynamics (REMD) has become a valuable tool in studying complex biomolecular systems. However, its application on distributed computing grids is limited by the heterogeneity of this environment. In this study, we propose a REMD implementation referred to as greedy REMD (gREMD) suitable for computations on heterogeneous grids. To decentralize replica management, gREMD utilizes a precomputed schedule of exchange attempts between temperatures. Our comparison of gREMD against standard REMD suggests four main conclusions. First, gREMD accelerates grid REMD simulations by as much as 40 %. Second, gREMD increases CPU utilization rates in grid REMD by up to 60 %. Third, we argue that gREMD is expected to maintain approximately constant CPU utilization rates and simulation wall-clock times with the increase in the number of replicas. Finally, we show that gREMD correctly implements the REMD algorithm and reproduces the conformational ensemble of a short peptide sampled in our previous standard REMD simulations. We believe that gREMD can find its place in large-scale REMD simulations on heterogeneous computing grids.

Graphical Abstract

Standard replica exchange molecular dynamics (REMD) typically requires all replicas to complete prior to initiation of the replica exchange protocol. Greedy REMD decentralizes this process and therefore only requires a replica and its predetermined exchange partner to have finished simulations prior to initiating replica exchange. Because greedy REMD reduces the idle time associated with replica exchange tasks, it becomes particularly well suited for performing REMD on heterogeneous distributed computing environments.

Keywords

Replica exchange molecular dynamics Conformational sampling Distributed grid-based simulations Decentralized replica management Aβ peptide 

Notes

Acknowledgments

This work was supported by the National Institute on Aging (National Institutes of Health) (grant R41 AG044022). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute on Aging or the National Institutes of Health.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Christopher Lockhart
    • 1
  • James O’Connor
    • 2
  • Steven Armentrout
    • 2
  • Dmitri K. Klimov
    • 1
  1. 1.School of Systems BiologyGeorge Mason UniversityManassasUSA
  2. 2.Parabon Computation Inc.RestonUSA

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