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J Comput Chem. 2014 Jul 5;35(18):1347-55. doi: 10.1002/jcc.23619. Epub 2014 Apr 28.

Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT.

Author information

1
Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, 223-8522, Japan.

Abstract

A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically. We tested the 3D-RISM calculation on the large and fine calculation cell (2048(3) grid points) on 16,384 nodes, each having eight CPU cores. The new 3D-RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D-RISM program is effective to analyze the hydration properties of the large biomolecular systems.

KEYWORDS:

3D-FFT; 3D-RISM theory; massively parallel machine

PMID:
24771232
DOI:
10.1002/jcc.23619
[Indexed for MEDLINE]

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