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231224s2016 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.24318
|2 doi
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|a pubmed24n0860.xml
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|a eng
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|a Takano, Yu
|e verfasserin
|4 aut
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|a Development of massive multilevel molecular dynamics simulation program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the elucidation of protein functions
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|c 2016
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
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|a ƒa Online-Ressource
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|a Date Completed 13.12.2016
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|a Date Revised 09.01.2021
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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|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
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|a News
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|a Research Support, Non-U.S. Gov't
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|a K computer
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|a QM/MM-MD simulation
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|a massively parallel computations
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|a parallelization ratio
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|a speedup
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|a Luminescent Proteins
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|a Nakata, Kazuto
|e verfasserin
|4 aut
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|a Yonezawa, Yasushige
|e verfasserin
|4 aut
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|a Nakamura, Haruki
|e verfasserin
|4 aut
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 37(2016), 12 vom: 05. Mai, Seite 1125-32
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|x 1096-987X
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|g volume:37
|g year:2016
|g number:12
|g day:05
|g month:05
|g pages:1125-32
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|u http://dx.doi.org/10.1002/jcc.24318
|3 Volltext
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