Parametrizing coarse grained models for molecular systems at equilibrium

Handle URI:
http://hdl.handle.net/10754/622583
Title:
Parametrizing coarse grained models for molecular systems at equilibrium
Authors:
Kalligiannaki, Evangelia; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plecháč, P.; Harmandaris, V.
Abstract:
Hierarchical 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.
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
Kalligiannaki 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.
Publisher:
Springer Nature
Journal:
The European Physical Journal Special Topics
Issue Date:
18-Oct-2016
DOI:
10.1140/epjst/e2016-60145-x
Type:
Article
ISSN:
1951-6355; 1951-6401
Appears in Collections:
Articles; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorKalligiannaki, Evangeliaen
dc.contributor.authorChazirakis, A.en
dc.contributor.authorTsourtis, A.en
dc.contributor.authorKatsoulakis, M. A.en
dc.contributor.authorPlecháč, P.en
dc.contributor.authorHarmandaris, V.en
dc.date.accessioned2017-01-02T09:55:31Z-
dc.date.available2017-01-02T09:55:31Z-
dc.date.issued2016-10-18en
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.en
dc.identifier.issn1951-6355en
dc.identifier.issn1951-6401en
dc.identifier.doi10.1140/epjst/e2016-60145-xen
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.en
dc.publisherSpringer Natureen
dc.titleParametrizing coarse grained models for molecular systems at equilibriumen
dc.typeArticleen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.identifier.journalThe European Physical Journal Special Topicsen
dc.contributor.institutionDepartment of Mathematics and Applied Mathematics University of Crete, Heraklion, Greeceen
dc.contributor.institutionDepartment of Mathematics and Statistics, University of Massachusetts at Amherst, Amherst, United Statesen
dc.contributor.institutionMathematical Sciences, University of Delaware, Newark, Delaware, United Statesen
dc.contributor.institutionInstitute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas, IACM/FORTH, G71110, Heraklion, Greeceen
kaust.authorKalligiannaki, Evangeliaen
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