|
|
|
|
| LEADER |
01000naa a22002652 4500 |
| 001 |
NLM237731495 |
| 003 |
DE-627 |
| 005 |
20231224112258.0 |
| 007 |
cr uuu---uuuuu |
| 008 |
231224s2014 xx |||||o 00| ||eng c |
| 024 |
7 |
|
|a 10.1002/jcc.23619
|2 doi
|
| 028 |
5 |
2 |
|a pubmed24n0792.xml
|
| 035 |
|
|
|a (DE-627)NLM237731495
|
| 035 |
|
|
|a (NLM)24771232
|
| 040 |
|
|
|a DE-627
|b ger
|c DE-627
|e rakwb
|
| 041 |
|
|
|a eng
|
| 100 |
1 |
|
|a Maruyama, Yutaka
|e verfasserin
|4 aut
|
| 245 |
1 |
0 |
|a Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT
|
| 264 |
|
1 |
|c 2014
|
| 336 |
|
|
|a Text
|b txt
|2 rdacontent
|
| 337 |
|
|
|a ƒaComputermedien
|b c
|2 rdamedia
|
| 338 |
|
|
|a ƒa Online-Ressource
|b cr
|2 rdacarrier
|
| 500 |
|
|
|a Date Completed 24.04.2015
|
| 500 |
|
|
|a Date Revised 06.06.2014
|
| 500 |
|
|
|a published: Print-Electronic
|
| 500 |
|
|
|a Citation Status MEDLINE
|
| 520 |
|
|
|a Copyright © 2014 Wiley Periodicals, Inc.
|
| 520 |
|
|
|a 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
|
| 650 |
|
4 |
|a Journal Article
|
| 650 |
|
4 |
|a Research Support, Non-U.S. Gov't
|
| 650 |
|
4 |
|a 3D-FFT
|
| 650 |
|
4 |
|a 3D-RISM theory
|
| 650 |
|
4 |
|a massively parallel machine
|
| 650 |
|
7 |
|a Peptides
|2 NLM
|
| 650 |
|
7 |
|a Plant Proteins
|2 NLM
|
| 650 |
|
7 |
|a Polymers
|2 NLM
|
| 650 |
|
7 |
|a chymotrypsin inhibitor 2
|2 NLM
|
| 700 |
1 |
|
|a Yoshida, Norio
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Tadano, Hiroto
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Takahashi, Daisuke
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Sato, Mitsuhisa
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Hirata, Fumio
|e verfasserin
|4 aut
|
| 773 |
0 |
8 |
|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 35(2014), 18 vom: 05. Juli, Seite 1347-55
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
|
| 773 |
1 |
8 |
|g volume:35
|g year:2014
|g number:18
|g day:05
|g month:07
|g pages:1347-55
|
| 856 |
4 |
0 |
|u http://dx.doi.org/10.1002/jcc.23619
|3 Volltext
|
| 912 |
|
|
|a GBV_USEFLAG_A
|
| 912 |
|
|
|a SYSFLAG_A
|
| 912 |
|
|
|a GBV_NLM
|
| 912 |
|
|
|a GBV_ILN_350
|
| 951 |
|
|
|a AR
|
| 952 |
|
|
|d 35
|j 2014
|e 18
|b 05
|c 07
|h 1347-55
|