title: Development of massive multilevel molecular dynamics simulation program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the elucidation of protein functions.
abstract: 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.
authors.affiliation: Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.|Department of Frontier Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima, 731-3194, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Takano
authors.affiliation: 1st Government and Public Solutions Division, NEC Corporation, 5-7-1, Shiba, Minato-Ku, Tokyo, 108-8001, Japan.
authors.forename: Kazuto
authors.initials: K
authors.lastname: Nakata
authors.affiliation: Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.|High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, 930 Nishimitani Kinokawa, Wakayama, 649-6493, Japan.
authors.forename: Yasushige
authors.initials: Y
authors.lastname: Yonezawa
authors.affiliation: Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
mesh_terms: D008164:Luminescent Proteins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012984:Software; D014867:Water / Q000737:chemistry
chemical_list: D008164:Luminescent Proteins; D014867:Water
keywords: K computer; QM/MM-MD simulation; massively parallel computations; parallelization ratio; speedup