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 language | English |
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Pages (from-to) | 446-456 |
Number of pages | 11 |
Journal | Journal of Computational Science |
Volume | 17 |
Issue number | part 2 |
Early online date | 24 Mar 2016 |
DOIs | |
Publication status | Published - 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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Dive into the research topics of 'Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution'. Together they form a unique fingerprint.Datasets
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Run Input file for MD simulation after 100ps at 200K (9f-3.tpr)
Nerukh, D. (Creator), Tarasova, E. (Contributor), Farafonov, V. (Contributor), Korotkin, I. (Contributor) & Karabasov, S. (Contributor), Aston Data Explorer, 24 Mar 2016
DOI: 10.17036/cfe11d20-c679-4952-8c95-ba2a7c87324d, https://www.sciencedirect.com/science/article/abs/pii/S1877750316300333
Dataset
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Run Input file for MD simulation after 1ns at 300K(15f-3.tpr)
Nerukh, D. (Creator), Tarasova, E. (Contributor), Farafonov, V. (Contributor), Korotkin, I. (Contributor) & Karabasov, S. (Contributor), Aston Data Explorer, 24 Mar 2016
DOI: 10.17036/b0629895-8312-4d04-8273-33a07f1db5d8, https://www.sciencedirect.com/science/article/abs/pii/S1877750316300333
Dataset