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dc.contributor.authorSomani, Sandeepen
dc.contributor.authorOkamoto, Yukoen
dc.contributor.authorBallard, Andrew Jen
dc.contributor.authorWales, Daviden
dc.date.accessioned2015-08-28T13:42:28Z
dc.date.available2015-08-28T13:42:28Z
dc.date.issued2015-05-12en
dc.identifier.citationJournal of Physical Chemistry B, 2015, 119 (20), pp 6155–6169 DOI: 10.1021/acs.jpcb.5b01800en
dc.identifier.issn1520-6106
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/250404
dc.description.abstractWe present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys. 2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide.
dc.description.sponsorshipThis research was funded by the European Research Council and EPSRC grant EP/I001352/1. Y.O. was supported, in part, by the JSPS Grant-in-Aid for Scientific Research on Innovative Areas (“Dynamical Ordering and Integrated Functions”).
dc.languageEnglishen
dc.language.isoenen
dc.publisherAmerican Chemical Society
dc.rightsAttribution 2.0 UK: England & Wales*
dc.rights.urihttp://creativecommons.org/licenses/by/2.0/uk/*
dc.titleEquilibrium Molecular Thermodynamics from Kirkwood Samplingen
dc.typeArticle
dc.description.versionThis is the final published version. It first appeared at http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b01800.en
prism.endingPage6169
prism.publicationDate2015en
prism.publicationNameJournal of Physical Chemistry Ben
prism.startingPage6155
prism.volume119en
dc.rioxxterms.funderEPSRC
dc.rioxxterms.funderEP/I001352/1
rioxxterms.versionofrecord10.1021/acs.jpcb.5b01800en
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2015-05-12en
dc.contributor.orcidWales, David [0000-0002-3555-6645]
dc.identifier.eissn1520-5207
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idEPSRC (EP/I001352/1)


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Attribution 2.0 UK: England & Wales
Except where otherwise noted, this item's licence is described as Attribution 2.0 UK: England & Wales