Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: 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 re 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.  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.
['Yu Takano', 'Kazuto Nakata', 'Yasushige Yonezawa', 'Haruki Nakamura']
I am writing a research paper on a idea Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions
[{"from": "human", "value": "I am writing a research paper on a idea Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions"}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: A massively parallel program for quantum mechanical\u2010molecular 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 re 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.  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."}]