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 journalArticle

Abstract

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
Volume17
Issue numberpart 2
Early online date24 Mar 2016
DOIs
Publication statusPublished - Nov 2016

Bibliographical note

© 2016, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/

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

Keywords

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

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