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    Parametrizing coarse grained models for molecular systems at equilibrium

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    Type
    Article
    Authors
    Kalligiannaki, Evangelia
    Chazirakis, A.
    Tsourtis, A.
    Katsoulakis, M. A.
    Plecháč, P.
    Harmandaris, V.
    KAUST Department
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Date
    2016-10-10
    Online Publication Date
    2016-10-10
    Print Publication Date
    2016-10
    Permanent link to this record
    http://hdl.handle.net/10754/622583
    
    Metadata
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    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.
    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
    DOI
    10.1140/epjst/e2016-60145-x
    ae974a485f413a2113503eed53cd6c53
    10.1140/epjst/e2016-60145-x
    Scopus Count
    Collections
    Articles; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

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