Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation

Whittaker, John; Site, Luigi Delle

doi:10.1103/physrevresearch.1.033099

Cited by 16 publications

(15 citation statements)

References 26 publications

(38 reference statements)

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“…The AdResS analysis, by identifying the minimal AT region, of about 0.7nm from the surface of the membrane, within which the membrane has a direct effect on the structural properties of water (and vice versa), reproduces results of a reference full atomistic simulation and of recent experiments (see the detailed discussion in Ref. [77]).…”

Section: Study Of the Hydration Shell Of A Membrane With The Open System Protocol Of Adresssupporting

confidence: 59%

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From adaptive resolution to molecular dynamics of open systems

et al. 2021

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We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method’s advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments. Graphic abstract

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Section: Study Of the Hydration Shell Of A Membrane With The Open System Protocol Of Adresssupporting

confidence: 59%

“…In Ref. [77] the AdResS approach with tracers has been applied to the hydration of a DPPC bilayer. The atomistic system of reference consists of a bilayer of 180 (90 per leaflet) DPPC molecules, solvated with 52470 water molecules (see Fig.…”

Section: Study Of the Hydration Shell Of A Membrane With The Open System Protocol Of Adressmentioning

confidence: 99%

From adaptive resolution to molecular dynamics of open systems

et al. 2021

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“…[ 175 ] Finally, an even more drastic simplification of the model of Krekeler et al., [ 183 ] in closer connection to the idea of open system embedded in a generic thermodynamic reservoir was pursued recently. [ 123,184 ] Here, the CG region is substituted by a reservoir of non‐interacting point‐particle (tracers). The AT region exchanges particles and energy with the reservoir in an adaptive manner as in the standard AdResS (see panel (c) of Figure 1).…”

Section: Adress and Open Systems Modelsmentioning

confidence: 99%

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

Site

Praprotnik

Bell

et al. 2020

Advcd Theory and Sims

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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.

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“…The abrupt coupling approach allows for efficient simulations of complex systems such as, for example, hydrated biological membranes. [16] While the standard atomistic simulation would require a sizable computational effort, the AdResS simulation, due to the drastically reduced number of degrees of freedom, runs at a reduced computational cost. It must be noticed that the initial calibration and validation of In panel (c) it is shown the x-direction along which the change of resolution occurs and the vector n, normal to the coupling boundaries, that defines the direction of the thermodynamic force.…”

Section: Introductionmentioning

confidence: 99%

“…The computational cost of such test systems, even at fully atomistic level, is negligible (see e.g., refs. [16][17][18]).…”

Section: Introductionmentioning

confidence: 99%

Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems

Gholami

Höfling

Klein

et al. 2021

Advcd Theory and Sims

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The adaptive resolution simulation (AdResS) technique couples regions with different molecular resolutions and allows the exchange of molecules between different regions in an adaptive fashion. The latest development of the technique allows to abruptly couple the atomistically resolved region with a region of non‐interacting point‐like particles. The abrupt set‐up is derived having in mind the idea of the atomistically resolved region as an open system embedded in a large reservoir at a given macroscopic state. In this work, starting from the idea of open systems, the authors derive thermodynamic relations for AdResS which justify conceptually and numerically the claim of AdResS as a technique for simulating open systems. In particular, the relation between the chemical potential of the AdResS set‐up and that of its reference fully atomistic simulation is derived. The implication of this result is that the grand potential of AdResS can be explicitly written and thus, from a statistical mechanics point of view, the atomistically resolved region of AdResS can be identified with a well‐defined open system.

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Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation

Cited by 16 publications

References 26 publications

From adaptive resolution to molecular dynamics of open systems

From adaptive resolution to molecular dynamics of open systems

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

Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems

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