Development of the third generation density functional calculation method and study of Born-Oppenheimer molecular dynamics method on protein
| Project/Area Number |
15H02046
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| Research Category |
Grant-in-Aid for Scientific Research (A)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Computational science
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| Research Institution | The University of Tokyo |
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Principal Investigator |
Sato Fumitoshi 東京大学, 生産技術研究所, 教授 (00235392)
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| Co-Investigator(Renkei-kenkyūsha) |
HIRANO Toshiyuki 東京大学, 生産技術研究所, 助教 (60451887)
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| Project Period (FY) |
2015-04-01 – 2018-03-31
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| Project Status |
Completed (Fiscal Year 2017)
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| Budget Amount *help |
¥38,740,000 (Direct Cost: ¥29,800,000、Indirect Cost: ¥8,940,000)
Fiscal Year 2017: ¥11,570,000 (Direct Cost: ¥8,900,000、Indirect Cost: ¥2,670,000)
Fiscal Year 2016: ¥11,570,000 (Direct Cost: ¥8,900,000、Indirect Cost: ¥2,670,000)
Fiscal Year 2015: ¥15,600,000 (Direct Cost: ¥12,000,000、Indirect Cost: ¥3,600,000)
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| Keywords | ハイパフォーマンス・コンピューティング / タンパク質 / 物性理論 / 量子化学 / 密度汎関数法 / 分子動力学法 / 原子電荷 / 蛋白質 / 量子化学計算 / 大規模計算 / 量子分子動力学法 |
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| Outline of Final Research Achievements |
We performed research and development of fundamental technology on canonical (standard) molecular orbital calculation and molecular dynamics simulation of proteins suitable for massively parallel computing environment. We improved ProteinDF which is our software of canonical molecular orbital calculation based on the third generation density functional method, and newly implemented and parallelized force calculation function. We developed a coupled system between ProteinDF and molecular dynamics calculation software Gromacs, and successfully demonstrated that this system works well by small proteins. In addition, in order to improve effectiveness of molecular dynamics simulation, we developed new atomic charges based on canonical molecular orbital calculation.
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Report
(4 results)
Research Products
(38 results)
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[Presentation] 量子分子生物学 春秋に富む2015
Author(s)
佐藤文俊, 平野敏行
Organizer
第15回 東京大学生命科学シンポジウム
Place of Presentation
東京大学, 文京区, 東京
Year and Date
2015-06-27
Related Report
Invited
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