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Open boundary molecular dynamics

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  • A. Representation of Molecular Systems Across Scales
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Abstract

This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system’s boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.

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Authors and Affiliations

  1. Departamento Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain

    R. Delgado-Buscalioni

  2. Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia

    J. Sablić & M. Praprotnik

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  1. R. Delgado-Buscalioni
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  2. J. Sablić
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  3. M. Praprotnik
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Correspondence to R. Delgado-Buscalioni.

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Delgado-Buscalioni, R., Sablić, J. & Praprotnik, M. Open boundary molecular dynamics. Eur. Phys. J. Spec. Top. 224, 2331–2349 (2015). https://doi.org/10.1140/epjst/e2015-02415-x

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  • DOI: https://doi.org/10.1140/epjst/e2015-02415-x

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