Literature DB >> 26616769

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics.

Prateek K Jha1, Rastko Sknepnek1, Guillermo Iván Guerrero-García1, Monica Olvera de la Cruz1.   

Abstract

We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (∼10(5)). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.

Entities:  

Year:  2010        PMID: 26616769     DOI: 10.1021/ct100365c

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  2 in total

1.  Non-Ewald methods: theory and applications to molecular systems.

Authors:  Ikuo Fukuda; Haruki Nakamura
Journal:  Biophys Rev       Date:  2012-08-02

2.  Appraisal of Bioactive Compounds of Betel Fruit as Antimalarial Agents by Targeting Plasmepsin 1 and 2: A Computational Approach.

Authors:  Trina Ekawati Tallei; Billy Johnson Kepel; Mohammed Alorabi; Ahmed M El-Shehawi; Widdhi Bodhi; Sefren Geiner Tumilaar; Ismail Celik; Gomaa Mostafa-Hedeab; Amany Abdel-Rahman Mohamed; Talha Bin Emran
Journal:  Pharmaceuticals (Basel)       Date:  2021-12-09
  2 in total

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