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Article: Combine Umbrella Sampling with Integrated Tempering Method for Efficient and Accurate Calculation of Free Energy Changes of Complex Energy Surface

TitleCombine Umbrella Sampling with Integrated Tempering Method for Efficient and Accurate Calculation of Free Energy Changes of Complex Energy Surface
Authors
Issue Date2014
Citation
Journal of Chemical Physics, 2014, v. 141, p. 044108 How to Cite?
AbstractUmbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when there exist multiple parallel channels along the reaction coordinate or hidden barriers in directions perpendicular to the reaction coordinate, it is difficult for conventional umbrella sampling to reach convergent sampling within limited simulation time. Here, we propose an approach to combine umbrella sampling with the integrated tempering sampling method. The umbrella sampling method is applied to chemically more relevant degrees of freedom that possess significant barriers. The integrated tempering sampling method is used to facilitate the sampling of other degrees of freedom which may possess statistically non-negligible barriers. The combined method is applied to two model systems, butane and ACE-NME molecules, and shows significantly improved sampling efficiencies as compared to standalone conventional umbrella sampling or integrated tempering sampling approaches. Further analyses suggest that the enhanced performance of the new method come from the complemented advantages of umbrella sampling with a well-defined reaction coordinate and integrated tempering sampling in orthogonal space. Therefore, the combined approach could be useful in the simulation of biomolecular processes, which often involves sampling of complex rugged energy landscapes.
Persistent Identifierhttp://hdl.handle.net/10722/200501
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorYang, Men_US
dc.contributor.authorYang, Len_US
dc.contributor.authorGao, Yen_US
dc.contributor.authorHu, Hen_US
dc.date.accessioned2014-08-21T06:48:45Z-
dc.date.available2014-08-21T06:48:45Z-
dc.date.issued2014-
dc.identifier.citationJournal of Chemical Physics, 2014, v. 141, p. 044108en_US
dc.identifier.urihttp://hdl.handle.net/10722/200501-
dc.description.abstractUmbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when there exist multiple parallel channels along the reaction coordinate or hidden barriers in directions perpendicular to the reaction coordinate, it is difficult for conventional umbrella sampling to reach convergent sampling within limited simulation time. Here, we propose an approach to combine umbrella sampling with the integrated tempering sampling method. The umbrella sampling method is applied to chemically more relevant degrees of freedom that possess significant barriers. The integrated tempering sampling method is used to facilitate the sampling of other degrees of freedom which may possess statistically non-negligible barriers. The combined method is applied to two model systems, butane and ACE-NME molecules, and shows significantly improved sampling efficiencies as compared to standalone conventional umbrella sampling or integrated tempering sampling approaches. Further analyses suggest that the enhanced performance of the new method come from the complemented advantages of umbrella sampling with a well-defined reaction coordinate and integrated tempering sampling in orthogonal space. Therefore, the combined approach could be useful in the simulation of biomolecular processes, which often involves sampling of complex rugged energy landscapes.en_US
dc.languageengen_US
dc.relation.ispartofJournal of Chemical Physicsen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsCopyright (2014) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in (citation of published article) and may be found at (http://dx.doi.org/10.1063/1.4887340).-
dc.titleCombine Umbrella Sampling with Integrated Tempering Method for Efficient and Accurate Calculation of Free Energy Changes of Complex Energy Surfaceen_US
dc.typeArticleen_US
dc.identifier.emailYang, M: mjyang@hku.hken_US
dc.identifier.emailHu, H: haohu@hku.hken_US
dc.identifier.authorityHu, H=rp00707en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1063/1.4887340en_US
dc.identifier.pmid25084882-
dc.identifier.hkuros234704en_US
dc.identifier.volume141en_US
dc.identifier.spage044108en_US
dc.identifier.epage044108en_US
dc.identifier.isiWOS:000340712200016-

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