Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks

67Citations
Citations of this article
59Readers
Mendeley users who have this article in their library.

This article is free to access.

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. Copyright © 2012 Wiley Periodicals, Inc.

Cite

CITATION STYLE

APA

Zhao, Y., De Nicola, A., Kawakatsu, T., & Milano, G. (2012). Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks. Journal of Computational Chemistry, 33(8), 868–880. https://doi.org/10.1002/jcc.22883

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free