Literature DB >> 21186852

The polarizable point dipoles method with electrostatic damping: implementation on a model system.

Jonàs Sala1, Elvira Guàrdia, Marco Masia.   

Abstract

Recently, the use of polarizable force fields in Molecular Dynamics simulations has been gaining importance, since they allow a better description of heterogeneous systems compared to simple point charges force fields. Among the various techniques developed in the last years the one based on polarizable point dipoles represents one of the most used. In this paper, we review the basic technical issues of the method, illustrating the way to implement intramolecular and intermolecular damping of the electrostatic interactions, either with and without the Ewald summation method. We also show how to reduce the computational overhead for evaluating the dipoles, introducing to the state-of-the-art methods: the extended Lagrangian method and the always stable predictor corrector method. Finally we discuss the importance of screening the electrostatic interactions at short range, defending this technique against simpler approximations usually made. We compare results of density functional theory and classical force field-based Molecular Dynamics simulations of chloride in water.

Entities:  

Mesh:

Substances:

Year:  2010        PMID: 21186852     DOI: 10.1063/1.3511713

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


  7 in total

1.  Polarizable molecular dynamics in a polarizable continuum solvent.

Authors:  Filippo Lipparini; Louis Lagardère; Christophe Raynaud; Benjamin Stamm; Eric Cancès; Benedetta Mennucci; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

2.  Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.

Authors:  Louis Lagardère; Filippo Lipparini; Étienne Polack; Benjamin Stamm; Éric Cancès; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2014-02-28       Impact factor: 6.006

3.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

4.  A comparison of sodium and hydrogen halides at the air-water interface.

Authors:  Collin D Wick
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

5.  Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

Authors:  Pengyu Ren; Chuanjie Wu; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2011-10-11       Impact factor: 6.006

6.  A Benchmark Protocol for DFT Approaches and Data-Driven Models for Halide-Water Clusters.

Authors:  Raúl Rodríguez-Segundo; Daniel J Arismendi-Arrieta; Rita Prosmiti
Journal:  Molecules       Date:  2022-03-02       Impact factor: 4.411

7.  Notes on simulating two-dimensional Raman and terahertz-Raman signals with a full molecular dynamics simulation approach.

Authors:  Hironobu Ito; Ju-Yeon Jo; Yoshitaka Tanimura
Journal:  Struct Dyn       Date:  2015-10-06       Impact factor: 2.920

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.