Literature DB >> 18205455

Modeling diffusive dynamics in adaptive resolution simulation of liquid water.

Silvina Matysiak1, Cecilia Clementi, Matej Praprotnik, Kurt Kremer, Luigi Delle Site.   

Abstract

We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS, we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of the here relevant structural, thermodynamical, and dynamical properties, i.e., radial distribution functions, pressure, temperature, and diffusion, of liquid water at ambient conditions.

Entities:  

Year:  2008        PMID: 18205455     DOI: 10.1063/1.2819486

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  4 in total

1.  Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.

Authors:  Nikolai D Petsev; L Gary Leal; M Scott Shell
Journal:  J Chem Phys       Date:  2015-01-28       Impact factor: 3.488

Review 2.  Adaptive resolution simulations of biomolecular systems.

Authors:  Julija Zavadlav; Staš Bevc; Matej Praprotnik
Journal:  Eur Biophys J       Date:  2017-09-13       Impact factor: 1.733

3.  Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting.

Authors:  Stephan Thaler; Julija Zavadlav
Journal:  Nat Commun       Date:  2021-11-25       Impact factor: 14.919

Review 4.  From adaptive resolution to molecular dynamics of open systems.

Authors:  Robinson Cortes-Huerto; Matej Praprotnik; Kurt Kremer; Luigi Delle Site
Journal:  Eur Phys J B       Date:  2021-09-23       Impact factor: 1.500

  4 in total

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