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dc.contributor.authorKalligiannaki, Evangelia
dc.contributor.authorChazirakis, A.
dc.contributor.authorTsourtis, A.
dc.contributor.authorKatsoulakis, M. A.
dc.contributor.authorPlecháč, P.
dc.contributor.authorHarmandaris, V.
dc.date.accessioned2017-01-02T09:55:31Z
dc.date.available2017-01-02T09:55:31Z
dc.date.issued2016-10-18
dc.identifier.citationKalligiannaki E, Chazirakis A, Tsourtis A, Katsoulakis MA, Plecháč P, et al. (2016) Parametrizing coarse grained models for molecular systems at equilibrium. The European Physical Journal Special Topics 225: 1347–1372. Available: http://dx.doi.org/10.1140/epjst/e2016-60145-x.
dc.identifier.issn1951-6355
dc.identifier.issn1951-6401
dc.identifier.doi10.1140/epjst/e2016-60145-x
dc.identifier.urihttp://hdl.handle.net/10754/622583
dc.description.abstractHierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.
dc.publisherSpringer Nature
dc.titleParametrizing coarse grained models for molecular systems at equilibrium
dc.typeArticle
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalThe European Physical Journal Special Topics
dc.contributor.institutionDepartment of Mathematics and Applied Mathematics University of Crete, Heraklion, Greece
dc.contributor.institutionDepartment of Mathematics and Statistics, University of Massachusetts at Amherst, Amherst, United States
dc.contributor.institutionMathematical Sciences, University of Delaware, Newark, Delaware, United States
dc.contributor.institutionInstitute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas, IACM/FORTH, G71110, Heraklion, Greece
kaust.personKalligiannaki, Evangelia


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