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dc.contributor.authorFernández-Pendás M.
dc.contributor.authorEscribano B.
dc.contributor.authorRadivojevic T.
dc.contributor.authorAkhmatskaya E.
dc.date.accessioned2016-06-13T13:32:22Z
dc.date.available2016-06-13T13:32:22Z
dc.date.issued2014-12-31
dc.identifier.issn1610-2940
dc.identifier.urihttp://hdl.handle.net/20.500.11824/167
dc.description.abstractAdaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines Andersen barostat with GSHMC to enable molecular simulations in the environment natural for biological applications, namely, at constant pressure and constant temperature. Generalized Hybrid Monte Carlo methods are designed to maintain constant temperature and volume and extending their functionality to preserving pressure is not trivial. The theoretical formulation of NPT-GSHMC was previously introduced. Our main contribution is the implementation of this methodology in the GROMACS molecular simulation package and the evaluation of properties of NPT-GSHMC, such as accuracy, performance, effectiveness for real physical systems in comparison with well-established molecular simulation techniques. Benchmarking tests are presented and the obtained preliminary results are promising. For the first time, the generalized hybrid Monte Carlo simulations at constant pressure are available within the popular open source molecular dynamics software package.
dc.formatapplication/pdf
dc.languageeng
dc.publisherJournal of Molecular Modeling
dc.relationES/6PN/MTM2011-24766
dc.relationES/1PE/SEV-2013-0323
dc.relationES/6PN/MTM2010-18318
dc.rightsinfo:eu-repo/semantics/openAccess
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/3.0/es/
dc.subjectaccuracy
dc.subjectArticle
dc.subjectbarostat
dc.subjectconstant pressure
dc.subjectgeneralized shadow hybrid monte carl simulation
dc.subjectmolecular dynamics
dc.subjectMonte Carlo method
dc.subjectpressure
dc.subjecttemperature
dc.subjectcontrolled study
dc.subjectGeneralized Shadow Hybrid Monte Carlo
dc.subjectmeasurement accuracy
dc.subjectmethodology
dc.subjectoscillation
dc.subjectpriority journal
dc.subjectquality control
dc.subjectsimulation
dc.subjecttheoretical study
dc.subjectvillin
dc.titleConstant pressure hybrid Monte Carlo simulations in GROMACS
dc.typeinfo:eu-repo/semantics/article
dc.typeinfo:eu-repo/semantics/acceptedVersion
dc.identifier.doi10.1007/s00894-014-2487-y
dc.relation.publisherversionhttp://link.springer.com/article/10.1007%2Fs00894-014-2487-y


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