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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\u2010pVDZ and B3LYP\/cc\u2010pVDZ, and up to 10,000 core processors by the CASCI(16,16)\/6\u201031G** calculations. We also performed excited QM\/MM\u2010MD simulations on the chromophore of Sirius (SIRIUS) in water. Sirius is a pH\u2010insensitive and photo\u2010stable ultramarine fluorescent protein. Platypus accelerated on\u2010the\u2010fly excited\u2010state QM\/MM\u2010MD simulations for SIRIUS in water, using over 4000 core processors. In addition, it also succeeded in 50\u2010ps (200,000\u2010step) on\u2010the\u2010fly excited\u2010state QM\/MM\u2010MD simulations for the SIRIUS in water. \u00a9 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.24318","type":"journal-article","created":{"date-parts":[[2016,3,5]],"date-time":"2016-03-05T16:32:29Z","timestamp":1457195549000},"page":"1125-1132","source":"Crossref","is-referenced-by-count":7,"title":["Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions"],"prefix":"10.1002","volume":"37","author":[{"given":"Yu","family":"Takano","sequence":"first","affiliation":[{"name":"Research Center for State\u2010of\u2010the\u2010Art Functional Protein Analysis, Institute for Protein Research, Osaka University 3\u20102 Yamadaoka, Suita Osaka 565\u20100871 Japan"},{"name":"Department of Frontier Sciences, Graduate School of Information Sciences Hiroshima City University 3\u20104\u20101 Ozuka\u2010Higashi, Asa\u2010Minami\u2010Ku Hiroshima 731\u20103194 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazuto","family":"Nakata","sequence":"additional","affiliation":[{"name":"1st Government and Public Solutions Division NEC Corporation 5\u20107\u20101, Shiba Minato\u2010Ku Tokyo 108\u20108001 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasushige","family":"Yonezawa","sequence":"additional","affiliation":[{"name":"Research Center for State\u2010of\u2010the\u2010Art Functional Protein Analysis, Institute for Protein Research, Osaka University 3\u20102 Yamadaoka, Suita Osaka 565\u20100871 Japan"},{"name":"High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University 930 Nishimitani Kinokawa Wakayama 649\u20106493 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haruki","family":"Nakamura","sequence":"additional","affiliation":[{"name":"Research Center for State\u2010of\u2010the\u2010Art Functional Protein Analysis, Institute for Protein Research, Osaka University 3\u20102 Yamadaoka, Suita Osaka 565\u20100871 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2016,3,4]]},"reference":[{"volume-title":"Biochemistry","year":"2004","author":"Voet D.","key":"e_1_2_6_1_1"},{"key":"e_1_2_6_2_1","unstructured":"D.Sadava D. 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