TY - JOUR
T1 - Hybrid particle-field molecular dynamics simulations
T2 - Parallelization and benchmarks
AU - Zhao, Ying
AU - De Nicola, Antonio
AU - Kawakatsu, Toshihiro
AU - Milano, Giuseppe
PY - 2012/3/30
Y1 - 2012/3/30
N2 - 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.
AB - 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.
KW - coarse-graining
KW - molecular dynamics
KW - parallelization
UR - http://www.scopus.com/inward/record.url?scp=84862779907&partnerID=8YFLogxK
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U2 - 10.1002/jcc.22883
DO - 10.1002/jcc.22883
M3 - Article
C2 - 22278759
AN - SCOPUS:84862779907
VL - 33
SP - 868
EP - 880
JO - Journal of Computational Chemistry
JF - Journal of Computational Chemistry
SN - 0192-8651
IS - 8
ER -