Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT
Copyright © 2014 Wiley Periodicals, Inc.
| Publié dans: | Journal of computational chemistry. - 1984. - 35(2014), 18 vom: 05. Juli, Seite 1347-55 |
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| Auteur principal: | |
| Autres auteurs: | , , , , |
| Format: | Article en ligne |
| Langue: | English |
| Publié: |
2014
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| Accès à la collection: | Journal of computational chemistry |
| Sujets: | Journal Article Research Support, Non-U.S. Gov't 3D-FFT 3D-RISM theory massively parallel machine Peptides Plant Proteins Polymers chymotrypsin inhibitor 2 |
| Résumé: | Copyright © 2014 Wiley Periodicals, Inc. 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 |
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| Description: | Date Completed 24.04.2015 Date Revised 06.06.2014 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.23619 |