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

Yutaka Maruyama, Norio Yoshida, Hiroto Tadano, Daisuke Takahashi, Mitsuhisa Sato, Fumio Hirata

Research output: Contribution to journalArticle

17 Citations (Scopus)

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 (20483 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.

Original languageEnglish
Pages (from-to)1347-1355
Number of pages9
JournalJournal of Computational Chemistry
Volume35
Issue number18
DOIs
Publication statusPublished - Jul 5 2014

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Fourier Analysis
Fast Fourier transform
Parallel Implementation
Fast Fourier transforms
Supercomputers
Supercomputer
Benchmarking
Oligomerization
Parallelization
Molecular Dynamics Simulation
Hydration
Program processors
Molecular dynamics
Scalability
Parallel Machines
3D Model
Mutant
Computer simulation
Inhibitor
Benchmark

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Computational Mathematics

Cite this

Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT. / Maruyama, Yutaka; Yoshida, Norio; Tadano, Hiroto; Takahashi, Daisuke; Sato, Mitsuhisa; Hirata, Fumio.

In: Journal of Computational Chemistry, Vol. 35, No. 18, 05.07.2014, p. 1347-1355.

Research output: Contribution to journalArticle

Maruyama, Yutaka ; Yoshida, Norio ; Tadano, Hiroto ; Takahashi, Daisuke ; Sato, Mitsuhisa ; Hirata, Fumio. / Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT. In: Journal of Computational Chemistry. 2014 ; Vol. 35, No. 18. pp. 1347-1355.
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