Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution

Ivan Korotkin, Dmitry Nerukh, Elvira Tarasova, Vladimir Farafonov, Sergey Karabasov

    Research output: Contribution to journalArticlepeer-review


    A hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework based on the analogy with two-phase hydrodynamics has been extended to dynamically tracking the feature of interest at all-atom resolution. In the model, the hydrodynamics description is used as an effective boundary condition to close the molecular dynamics solution without resorting to standard periodic boundary conditions. The approach is implemented in a popular Molecular Dynamics package GROMACS and results for two biomolecular systems are reported. A small peptide dialanine and a complete capsid of a virus porcine circovirus 2 in water are considered and shown to reproduce the structural and dynamic properties compared to those obtained in theory, purely atomistic simulations, and experiment.
    Original languageEnglish
    Pages (from-to)446-456
    Number of pages11
    JournalJournal of Computational Science
    Issue numberpart 2
    Early online date24 Mar 2016
    Publication statusPublished - Nov 2016

    Bibliographical note

    © 2016, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

    Funding: EPSRC (EP/J004308/1); Royal Society of London; Royal Society of Chemistry; Royal Academy of Engineering; and Leverhulme Trust.


    • hybrid atomistic/continuum
    • multiscale
    • molecular dynamics
    • fluctuating hydrodynamics
    • dialanine
    • all-atom whole virus simulation
    • capsid
    • PCV2


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