Development of the third generation density functional calculation method and study of Born-Oppenheimer molecular dynamics method on protein

2017 Fiscal Year Final Research Report

• Project/Area Number: 15H02046
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Computational science
• Research Institution: The University of Tokyo
• Principal Investigator: Sato Fumitoshi 東京大学, 生産技術研究所, 教授 (00235392)
• Co-Investigator(Renkei-kenkyūsha): HIRANO Toshiyuki 東京大学, 生産技術研究所, 助教 (60451887)
• Project Period (FY): 2015-04-01 – 2018-03-31
• 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

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.

Free Research Field

理論化学