SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids

Zavadlav, Julija; Marrink, Siewert J.; Praprotnik, Matej

doi:10.1098/rsfs.2018.0075

Cited by 11 publications

(11 citation statements)

References 84 publications

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“…Important stimuli for the optimisation of coarse-grained methods come from the multiscale studies and from the papers that compare the results of DPD with other types of simulations and/or with mean-field predictions [189][190][191][192][193][194][195]. Spaeth et al [196] employed the implicit solvent Brownian dynamics (BD) using the parameters proposed earlier by Chen [197] and the explicit solvent DPD simulation.…”

Section: Studies Aimed At the Improvement Of Dpd Methodology And At Important Trends Of The Behaviourmentioning

confidence: 99%

DPD Modelling of the Self- and Co-Assembly of Polymers and Polyelectrolytes in Aqueous Media: Impact on Polymer Science

et al. 2022

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This review article is addressed to a broad community of polymer scientists. We outline and analyse the fundamentals of the dissipative particle dynamics (DPD) simulation method from the point of view of polymer physics and review the articles on polymer systems published in approximately the last two decades, focusing on their impact on macromolecular science. Special attention is devoted to polymer and polyelectrolyte self- and co-assembly and self-organisation and to the problems connected with the implementation of explicit electrostatics in DPD numerical machinery. Critical analysis of the results of a number of successful DPD studies of complex polymer systems published recently documents the importance and suitability of this coarse-grained method for studying polymer systems.

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Section: Studies Aimed At the Improvement Of Dpd Methodology And At Important Trends Of The Behaviourmentioning

confidence: 99%

DPD Modelling of the Self- and Co-Assembly of Polymers and Polyelectrolytes in Aqueous Media: Impact on Polymer Science

et al. 2022

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“…The adaptive resolution representation of the solvent served also for the calculation of solvation free energies of side-chain analogues, using the AdResS ( Fiorentini et al, 2017 ) or H-AdResS ( Korshunova and Carloni, 2021 ) scheme. Further applications of adaptive resolution simulation methods include the coupling of atomistic water with a supramolecular, MARTINI-style model ( Zavadlav et al, 2019 ), or even an ideal gas representation ( Kreis et al, 2015 ), which can also provide an innovative solution for solvation free energy calculation, by pulling the solute from the atomistic solvent region to the CG one ( Heidari et al, 2019 ).…”

Section: Coarse-grained Modeling: Resolution Distributionmentioning

confidence: 99%

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

Giulini

Rigoli

Mattiotti

et al. 2021

Front. Mol. Biosci.

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The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.

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“…[ 68 ] The computational burden is drastically alleviated by implicit solvent models but if one is interested in hydrodynamic interactions the inclusion of explicit solvent is in many cases unavoidable. [ 69,70 ]…”

Section: Molecular Dynamics (Md) and (Particle‐based) Multiscale Simumentioning

confidence: 99%

“…To this end, we have developed a dynamic clustering algorithm SWINGER that can concurrently assemble, disassemble, and reassemble water bundles, consisting of several water molecules. [ 69,124,125,134 ] Thus, it allows for a seamless coupling between standard atomistic and supramolecular water models in adaptive resolution simulations. Our multiscale approach paves the way for efficient multiscale simulations of biomolecular systems without compromising the accuracy of atomistic water models.…”

Section: Molecular Dynamics (Md) and (Particle‐based) Multiscale Simumentioning

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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SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids

Cited by 11 publications

References 84 publications

DPD Modelling of the Self- and Co-Assembly of Polymers and Polyelectrolytes in Aqueous Media: Impact on Polymer Science

DPD Modelling of the Self- and Co-Assembly of Polymers and Polyelectrolytes in Aqueous Media: Impact on Polymer Science

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

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

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