Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks

Authors

  • Ying Zhao,

    Corresponding author
    1. Dipartimento di Chimica e Biologia and NANOMATES, Research Centre for NANOMAterials and nanoTEchnology at Università di Salerno, I-84084 via Ponte don Melillo Fisciano (SA), Italy
    Current affiliation:
    1. State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, Liaoning 116023, China. E-mail: zhaoying@dicp.ac.cn
    • Dipartimento di Chimica e Biologia and NANOMATES, Research Centre for NANOMAterials and nanoTEchnology at Università di Salerno, I-84084 via Ponte don Melillo Fisciano (SA), Italy
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  • Antonio De Nicola,

    1. Dipartimento di Chimica e Biologia and NANOMATES, Research Centre for NANOMAterials and nanoTEchnology at Università di Salerno, I-84084 via Ponte don Melillo Fisciano (SA), Italy
    2. IMAST Scarl-Technological District in Polymer and Composite Engineering, P.le Fermi 1, 80055 Portici (NA), Italy
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  • Toshihiro Kawakatsu,

    1. Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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  • Giuseppe Milano

    Corresponding author
    1. Dipartimento di Chimica e Biologia and NANOMATES, Research Centre for NANOMAterials and nanoTEchnology at Università di Salerno, I-84084 via Ponte don Melillo Fisciano (SA), Italy
    2. IMAST Scarl-Technological District in Polymer and Composite Engineering, P.le Fermi 1, 80055 Portici (NA), Italy
    • Dipartimento di Chimica e Biologia and NANOMATES, Research Centre for NANOMAterials and nanoTEchnology at Università di Salerno, I-84084 via Ponte don Melillo Fisciano (SA), Italy
    Search for more papers by this author

  • How to cite this article: Y. Zhao, A. De Nicola, T. Kawakatsu, G. Milano, J. Comput. Chem. 2012, 33, 868-880. DOI: 10.1002/jcc.22883

Abstract

The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where self-consistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle-field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD-SCF program profiles, serial MD-SCF and parallel MD-SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs. © 2012 Wiley Periodicals, Inc.

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