|
|
|
|
| LEADER |
01000caa a22002652 4500 |
| 001 |
NLM258082682 |
| 003 |
DE-627 |
| 005 |
20250219193208.0 |
| 007 |
cr uuu---uuuuu |
| 008 |
231224s2016 xx |||||o 00| ||eng c |
| 024 |
7 |
|
|a 10.1002/jcc.24318
|2 doi
|
| 028 |
5 |
2 |
|a pubmed25n0860.xml
|
| 035 |
|
|
|a (DE-627)NLM258082682
|
| 035 |
|
|
|a (NLM)26940542
|
| 040 |
|
|
|a DE-627
|b ger
|c DE-627
|e rakwb
|
| 041 |
|
|
|a eng
|
| 100 |
1 |
|
|a Takano, Yu
|e verfasserin
|4 aut
|
| 245 |
1 |
0 |
|a Development of massive multilevel molecular dynamics simulation program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the elucidation of protein functions
|
| 264 |
|
1 |
|c 2016
|
| 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 13.12.2016
|
| 500 |
|
|
|a Date Revised 09.01.2021
|
| 500 |
|
|
|a published: Print-Electronic
|
| 500 |
|
|
|a Citation Status MEDLINE
|
| 520 |
|
|
|a © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
|
| 520 |
|
|
|a A massively parallel program for quantum mechanical-molecular mechanical (QM/MM) molecular dynamics simulation, called Platypus (PLATform for dYnamic Protein Unified Simulation), was developed to elucidate protein functions. The speedup and the parallelization ratio of Platypus in the QM and QM/MM calculations were assessed for a bacteriochlorophyll dimer in the photosynthetic reaction center (DIMER) on the K computer, a massively parallel computer achieving 10 PetaFLOPs with 705,024 cores. Platypus exhibited the increase in speedup up to 20,000 core processors at the HF/cc-pVDZ and B3LYP/cc-pVDZ, and up to 10,000 core processors by the CASCI(16,16)/6-31G** calculations. We also performed excited QM/MM-MD simulations on the chromophore of Sirius (SIRIUS) in water. Sirius is a pH-insensitive and photo-stable ultramarine fluorescent protein. Platypus accelerated on-the-fly excited-state QM/MM-MD simulations for SIRIUS in water, using over 4000 core processors. In addition, it also succeeded in 50-ps (200,000-step) on-the-fly excited-state QM/MM-MD simulations for the SIRIUS in water
|
| 650 |
|
4 |
|a News
|
| 650 |
|
4 |
|a Research Support, Non-U.S. Gov't
|
| 650 |
|
4 |
|a K computer
|
| 650 |
|
4 |
|a QM/MM-MD simulation
|
| 650 |
|
4 |
|a massively parallel computations
|
| 650 |
|
4 |
|a parallelization ratio
|
| 650 |
|
4 |
|a speedup
|
| 650 |
|
7 |
|a Luminescent Proteins
|2 NLM
|
| 650 |
|
7 |
|a Water
|2 NLM
|
| 650 |
|
7 |
|a 059QF0KO0R
|2 NLM
|
| 700 |
1 |
|
|a Nakata, Kazuto
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Yonezawa, Yasushige
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Nakamura, Haruki
|e verfasserin
|4 aut
|
| 773 |
0 |
8 |
|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 37(2016), 12 vom: 05. Mai, Seite 1125-32
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
|
| 773 |
1 |
8 |
|g volume:37
|g year:2016
|g number:12
|g day:05
|g month:05
|g pages:1125-32
|
| 856 |
4 |
0 |
|u http://dx.doi.org/10.1002/jcc.24318
|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 37
|j 2016
|e 12
|b 05
|c 05
|h 1125-32
|