Document Detail

Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks.
MedLine Citation:
PMID:  22278759     Owner:  NLM     Status:  Publisher    
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.
Ying Zhao; Antonio De Nicola; Toshihiro Kawakatsu; Giuseppe Milano
Related Documents :
22413059 - On quantum effects in a theory of biological evolution.
20697599 - Dynamic double layer effects on ac-induced dipoles of dielectric nanocolloids.
18299989 - A simulation study on the effect of thoracic conductivity inhomogeneities on sensitivit...
23496719 - Experimental verification of entropy cascade in two-dimensional electrostatic turbulenc...
20208869 - Electrooptic streak camera: theoretical analysis.
3177219 - Occupational and residential 60-hz electromagnetic fields and high-frequency electric t...
23187219 - Symbiotic two-component gap solitons.
9754679 - Real time analysis of lung sounds.
14650529 - A spatially explicit model simulating western corn rootworm (coleoptera: chrysomelidae)...
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-1-25
Journal Detail:
Title:  Journal of computational chemistry     Volume:  -     ISSN:  1096-987X     ISO Abbreviation:  -     Publication Date:  2012 Jan 
Date Detail:
Created Date:  2012-1-26     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9878362     Medline TA:  J Comput Chem     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
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.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

Previous Document:  A water-soluble calix[4]resorcinarene with L-pipecolinic acid groups as a chiral NMR solvating agent...
Next Document:  Oceaniovalibus guishaninsula gen. nov., sp. nov., A Marine Bacterium of the Family Rhodobacteraceae.