skip to main content
Idioma:
Primo Search
Clear Search Box
Search in: Busca Geral
Busca Avançada
Busca por Índices

Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions

Takano, Yu ; Nakata, Kazuto ; Yonezawa, Yasushige ; Nakamura, Haruki

Journal of computational chemistry, 2016-05, Vol.37 (12), p.1125-1132 [Periódico revisado por pares]

United States: Blackwell Publishing Ltd

Texto completo disponível

Citações Citado por
  • Título:
    Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions
  • Autor: Takano, Yu ; Nakata, Kazuto ; Yonezawa, Yasushige ; Nakamura, Haruki
  • Assuntos: Bacterial proteins ; Chemistry ; Computational chemistry ; Computer simulation ; Cores ; Fluorescence ; K computer ; Luminescent Proteins - chemistry ; Luminescent Proteins - metabolism ; massively parallel computations ; Mathematical analysis ; Mathematical models ; Microprocessors ; Molecular dynamics ; Molecular Dynamics Simulation ; Multilevel ; Parallel processing ; Parallel programming ; parallelization ratio ; Photosynthesis ; Processors ; Proteins ; QM/MM-MD simulation ; Quantum mechanics ; Quantum physics ; Quantum Theory ; Simulation ; Software ; Software and Updates ; speedup ; Supercomputers ; Water - chemistry
  • É parte de: Journal of computational chemistry, 2016-05, Vol.37 (12), p.1125-1132
  • Notas: Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, Grant-in-Aid for Scientific Research on Innovative Areas "Transcription cycle" (to H. N.) - No. 24118001
    ark:/67375/WNG-J08Z9GR4-X
    Research and Development of the Next-Generation Integrated Simulation of Living Matter (a part of the Development and Use of the Next-Generation Supercomputer Project of MEXT); Contract grant sponsor: Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, Grant-in-Aid for Scientific Research on Innovative Areas "3D active-site science" (to Y. T.) - No. 26105012
    istex:876B3D9F6A12BFAF3E4613D36F5AFBCAFF451B37
    ArticleID:JCC24318
    SourceType-Other Sources-1
    ObjectType-Article-2
    ObjectType-News-1
    content type line 66
  • Descrição: 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. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. A massively parallel program for on‐the‐fly quantum mechanical‐molecular mechanical (QM/MM) molecular dynamics simulations, Platypus (PLATform for dYnamic Protein Unified Simulation), was developed for the elucidation of protein functions. The performances of Platypus were assessed for bacteriochlorophyll dimer and the chromophore of Sirius, a pH‐insensitive and photo‐stable ultramarine fluorescent protein, in water on the K computer. Platypus succeeded in massively parallel computations, using more than 10,000 core processors.
  • Editor: United States: Blackwell Publishing Ltd
  • Idioma: Inglês
Links
Voltar para lista de resultados

  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

Buscando em bases de dados remotas. Favor aguardar.