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 journalArticlepeer-review

20 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

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Computational Mathematics

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