title: Hybrid particle-field molecular dynamics simulations: parallelization and benchmarks.
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.
authors.affiliation: 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. yzhao@unisa.it
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhao
authors.forename: Antonio
authors.initials: A
authors.lastname: De Nicola
authors.forename: Toshihiro
authors.initials: T
authors.lastname: Kawakatsu
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Milano