Realization of variable molecular dynamics simulations by generalized cutoff method and double density dynamics
| Project/Area Number |
17K05143
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Computational science
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| Research Institution | University of Hyogo (2018-2020)
Osaka University (2017) |
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Principal Investigator |
Fukuda Ikuo 兵庫県立大学, シミュレーション学研究科, 特任教授 (40643185)
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| Co-Investigator(Kenkyū-buntansha) |
森次 圭 横浜市立大学, 生命医科学研究科, 特任准教授 (80599506)
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| Project Period (FY) |
2017-04-01 – 2021-03-31
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| Project Status |
Completed (Fiscal Year 2020)
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| Budget Amount *help |
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2019: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2018: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
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| Keywords | 分子動力学 / 相互作用計算 / 力学系 / 運動方程式 / サンプリング / 数値積分 / 数値計算 / 数値シミュレーション |
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| Outline of Final Research Achievements |
Molecular dynamics simulation involves two kinds of problems. The first one is that we must assume conditions on total charge of consisting atoms and on environment surrounding the target molecules. The second one is the difficulty in stable and easy realization of coupling between the target physical system and its arbitrary chosen environment system within a rigorous statistical physics approach. We have solved these problems to easily realize variable molecular dynamics simulations by developing a generalized cutoff method and by stabilizing double density dynamics. These methods ensure high accuracies and reduce the computational cost that is the bottleneck of the molecular dynamics simulation for a large system.
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| Academic Significance and Societal Importance of the Research Achievements |
分子動力学シミュレーションは，生体系における種々のメカニズムの解明やそれに基づいた薬物の設計等を可能にし，我々の生活に大きく影響を与え得る技術の一つになってきている．しかし，技術的問題に起因したシミュレーション条件についての制約が，より多様なシミュレーションの容易な実現を阻んでいる．これらの制約を除く技術を開発することで，現状では不可能な多様な用途のシミュレーションを可能にし，物理・化学の基礎科学分野のみならず，材料工学，環境工学，或いは薬学等を対象にする幅広い分野で容易に用いられための研究基盤の確立を目指すものである．
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Report
(5 results)
Research Products
(22 results)
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[Presentation] myPresto, computer-aided drug development software2019
Author(s)
Shinji Iida, Ikuo Fukuda, Junichi Higo , Kota Kasahara, Takashi Kurosawa, Tadaaki Mashimo, Kiyotaka Misoo, Yoshinori Wakabayasi, Ryuta Murakami, Chisato Kanai, Yusuke Sugihara, Mitsuhito Wada, Hironori Nakamura, Yoshifumi Fukunishi
Organizer
第57回日本生物物理学会年会
Related Report
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