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

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

研究成果: ジャーナルへの寄稿学術誌査読

26 被引用数 (Scopus)

抄録

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.

本文言語英語
ページ(範囲)1347-1355
ページ数9
ジャーナルJournal of Computational Chemistry
35
18
DOI
出版ステータス出版済み - 7月 5 2014

!!!All Science Journal Classification (ASJC) codes

  • 化学 (全般)
  • 計算数学

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