Hybrid particle-field molecular dynamics simulations parallelization and benchmarks

Hybrid particle-field molecular dynamics simulations : parallelization and benchmarks

Copyright © 2012 Wiley Periodicals, Inc.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 33(2012), 8 vom: 30. März, Seite 868-80
1. Verfasser: Zhao, Ying (VerfasserIn)
Weitere Verfasser: De Nicola, Antonio, Kawakatsu, Toshihiro, Milano, Giuseppe
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2012
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article
Beschreibung
Zusammenfassung:Copyright © 2012 Wiley Periodicals, Inc.
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
Beschreibung:Date Completed 18.06.2012
Date Revised 22.02.2012
published: Print-Electronic
Citation Status PubMed-not-MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.22883