A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

Korotkin, Ivan; Karabasov, Sergey A.; Nerukh, Dmitry; Markesteijn, Anton P.; Scukins, Arturs; Farafonov, Vladimir; Pavlov, Evgen

doi:10.1063/1.4923011

Cited by 19 publications

(44 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Detailed derivation of the above equations can be found in [6,7] but the following should be highlighted.…”

Section: X  mentioning

confidence: 99%

“…to smoothly enforce the same density and momentum both 'phases' which represent the same chemical substance. Further details of the full two-way coupling model are available in [6,7] and the current work focuses on a simpler, one-way coupling model where the equation for mixture averages are computed separately from the particles. Indeed, for macroscopically stationary liquids in the absence of major hydrodynamic gradients and away from solid boundaries, thermal fluctuations are the only source of macroscopic fluctuations in liquids described by the LandauLifshitz Fluctuating Hydrodynamics (LL-FH) model.…”

Section: The Underlying Two-way Coupling Approach and Its Reduction Tmentioning

confidence: 99%

“…Following [7], let us consider a solution domain of volume V0 which is broken down into elementary Eulerian cubical cells of volume V. Each cell has 6 faces 6 ,.., 1   and it is filled with the continuum part of the liquid and, at the same time, with the MD particles which correspond to the discrete representation of the same chemical substance. It is assumed that the continuum part of the nominally two-phase fluid has the same transport velocity as that of the mixture.…”

Section: The Underlying Two-way Coupling Approach and Its Reduction Tmentioning

confidence: 99%

“…  The flux terms can be calculated from the particle distributions at each point of the cell boundary either directly or approximately. In [6,7], for computing the cell-boundary values an interpolation method is used that is based on the particle distributions specified at the centres of adjacent volumes V in a finite-volume framework.…”

Section: The Underlying Two-way Coupling Approach and Its Reduction Tmentioning

confidence: 99%

“…In [7] a one-way coupling implementation of the same hybrid framework, which accounts for the effect of molecular dynamics on continuum hydrodynamics without the feedback, was considered and tested as an alternative open boundary treatment in the popular Molecular Dynamics (MD) package GROMACS [8]. In the current paper, the former implementation in GROMACS has been extended to dynamically tracking the atomistic-resolution features of interest.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

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

Korotkin

Nerukh

Tarasova

et al. 2016

Journal of Computational Science

Self Cite

View full text Add to dashboard Cite

Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution, Journal of Computational Science http://dx.doi.org/10. 1016/j.jocs.2016.03.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. HighlightsWe have recently suggested and implemented a new approach to the problem of computing liquids at multiple scales in space and time based on the two-phase hydrodynamics analogy. Instead of separating the system into parts using boundaries, in the current hybrid approach the liquid is described as a nominally two-phase system consisting of both particle and continuum at the same time and using the continuum part of the model as an effective opendomain boundary condition for atomistic simulations. For the current paper, the method has been extended to dynamically tracking the atomistic-resolution features of interest which can evolve in the flow. Simulations of two very different biomolecular systems have been performed using our hybrid method implemented in the framework of the popular open-source GROMACS software. For both examples, it has been shown that the hybrid model can preserve important properties of the molecular part of the system. For the problem of peptide diffusion in water, the method has allowed obtaining the value of diffusion coefficient which is very close to that one of the reference all-atom simulation. For the virus in water problem, the method has preserved the structure of the virus capsid despite a relatively thin layer of molecular water around the proteins constituting the capsid, and which is in contrast with the all-atom simulation with the standard periodic boundary conditions. 3 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.

show abstract

“…Detailed derivation of the above equations can be found in [6,7] but the following should be highlighted.…”

Section: X  mentioning

confidence: 99%

Section: The Underlying Two-way Coupling Approach and Its Reduction Tmentioning

confidence: 99%

Section: The Underlying Two-way Coupling Approach and Its Reduction Tmentioning

confidence: 99%

Section: The Underlying Two-way Coupling Approach and Its Reduction Tmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Korotkin

Nerukh

Tarasova

et al. 2016

Journal of Computational Science

Self Cite

View full text Add to dashboard Cite

show abstract

Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications

Site

Praprotnik

Bell

et al. 2020

Advcd Theory and Sims

View full text Add to dashboard Cite

This work is motivated by the goal of designing simulation software for technical devices that, at their functional core, rely on atomistic-scale processes embedded in a larger-scale fluid environment. The core of the problem is the conceptual and technical approach for coupling particle and continuum representations of a fluid. The state of the art for key aspects including physical modeling, mathematical formalization, computational implementation, and applications, is discussed and organized in a consistent picture across the relevant physical regimes.Key building blocks of the related developments that we will summarize and appraise in some detail below are i) finite volume FHD solvers following Bell, Donev, Garcia, Nonaka and colleagues [4] (see Section 2), ii) the "adaptive resolution simulation" (AdResS) approach that enables molecular dynamics simulations on limited size domains [5][6][7] (see Section 3), and iii) the recent mathematical formalization of open molecular systems by two of the authors [8] (see Section 4). In Section 5, we discuss scaling regimes and the rationale behind possible MD-FHD coupling strategies, finally, Section 6 is dedicated to the description of some representative examples, while Section 7 outlines future perspectives and summarizes our conclusions.

show abstract

A Thermostat‐Consistent Fully Coupled Molecular Dynamics—Generalized Fluctuating Hydrodynamics Model

Liu

Korotkin

Rao

et al. 2020

Advcd Theory and Sims

Self Cite

View full text Add to dashboard Cite

The previously developed multiscale method for concurrently coupling atomistic and continuum hydrodynamic representations of the same chemical substance is extended to consistently incorporate the Langevin‐type thermostat equations in the model. This allows not only to preserve the mass and momentum conservation laws based on the two‐phase flow analogy modeling framework but also to capture the correct local fluctuations and temperature in the pure atomistic region of the hybrid model. Numerical results for the test problem of equilibrium isothermal fluctuations of SPC/E water are presented. Advantages of using local thermostat equations adjusted for the multiresolution model for accurately capturing of the local water density in the atomistic part of the hybrid simulation domain are discussed. Comparisons with the reference pure all‐atom molecular dynamics simulations in GROMACS show that the suggested hybrid models are by a factor of 5–20 faster depending on the simulation domain size.

show abstract

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

Cited by 19 publications

References 61 publications

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

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

Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications

A Thermostat‐Consistent Fully Coupled Molecular Dynamics—Generalized Fluctuating Hydrodynamics Model

Contact Info

Product

Resources

About