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Improving replica exchange using driven scaling

J. Chem. Phys. 131, 174113 (2009); doi:10.1063/1.3259049

Published 6 November 2009

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Alexis J. Lee and Steven W. Rick
Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
Replica exchange is a powerful simulation method in which simulations are run at a series of temperatures, with the highest temperature chosen so phase space can be sampled efficiently. In order for swaps to be accepted, the energy distributions of adjacent replicas must have some overlap. This can create the need for many replicas for large systems. In this paper, we present a new method in which the potential energy is scaled by a parameter, which has an explicit time dependence. Scaling the potential energy broadens the distribution of energy and reduces the number of replicas necessary to span a given temperature range. We demonstrate that if the system is driven by the time-dependent potential sufficiently slowly, then equilibrium is maintained and energetic and structural properties are identical to those of conventional replica exchange. The method is tested using two systems, the alanine dipeptide and the trpzip2 polypeptide, both in water. ©2009 American Institute of Physics
History: Received 20 August 2009; accepted 15 October 2009; published 6 November 2009
Permalink: http://link.aip.org/link/?JCPSA6/131/174113/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.A-
    Theory, modeling and computer simulation in molecular biophysics
  • 87.15.B-
    Structure of biomolecules
  • 87.14.ef
    Peptides
  • 02.60.Pn
    Numerical optimization
  • YEAR: 2009

PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
Publisher:
AIP is a member of CrossRef AIP

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