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Realization of variable molecular dynamics simulations by generalized cutoff method and double density dynamics

Research Project

Project/Area Number 17K05143
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Computational science
Research InstitutionUniversity of Hyogo (2018-2020)
Osaka University (2017)

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)

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)
Project Period (FY) 2017-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
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)
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
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.

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.

Report

(5 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (22 results)

All 2021 2020 2019 2018 2017

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 7 results) Presentation (14 results) (of which Int'l Joint Research: 3 results,  Invited: 2 results) Book (1 results)

  • [Journal Article] Flexibility and cell permeability of cyclic Ras-inhibitor peptides revealed by coupled Nose Hoover equation2021

    • Author(s)
      Kei Moritsugu, Koh Takeuchi, Narutoshi Kamiya, Junichi Higo, Isao Yasumatsu, Yoshifumi Fukunishi and Ikuo Fukuda
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 61 Issue: 4 Pages: 1921-1930

    • DOI

      10.1021/acs.jcim.0c01427

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] On Ergodicity for Multi-Dimensional Harmonic Oscillator Systems with Nose--Hoover Type Thermostat2021

    • Author(s)
      Ikuo Fukuda, Kei Moritsugu, and Yoshifumi Fukunishi
    • Journal Title

      Regular and Chaotic Dynamics

      Volume: 26 Issue: 2 Pages: 183-204

    • DOI

      10.1134/s1560354721020064

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Temperature--Energy-Space Sampling Molecular Dynamics: Deterministic and Single-Replica Method Utilizing Continuous Temperature System2020

    • Author(s)
      Ikuo Fukuda and Kei Moritsugu
    • Journal Title

      J. Phys. A: Math. Theor.

      Volume: 53 Issue: 37 Pages: 375004-375004

    • DOI

      10.1088/1751-8121/aba027

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Robust, Symmetric Operator-Composition Integrator for the Berendsen Temperature-Control Molecular Dynamics Equation2020

    • Author(s)
      I. Fukuda, S. Queyroy S, and H. Nakamura
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 89 Issue: 6 Pages: 064004-064004

    • DOI

      10.7566/jpsj.89.064004

    • NAID

      40022254134

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Symmetric, Explicit Numerical Integrator for Molecular Dynamics Equations of Motion with a Generalized Friction2019

    • Author(s)
      Ikuo Fukuda
    • Journal Title

      J. Math. Phys.

      Volume: 60 Issue: 4 Pages: 042903-042903

    • DOI

      10.1063/1.5012871

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation2018

    • Author(s)
      Kasahara Kota、Sakuraba Shun、Fukuda Ikuo
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 122 Issue: 9 Pages: 2495-2503

    • DOI

      10.1021/acs.jpcb.7b10830

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Performance Evaluation of the Zero-Multipole Summation Method in Modern Molecular Dynamics2018

    • Author(s)
      Shun Sakuraba、Ikuo Fukuda
    • Journal Title

      Journal of Computational Chemistry

      Volume: 印刷中

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] Enhanced conformational sampling of cyclic peptide cyclorasin by coupled Nose--Hoover equation2020

    • Author(s)
      Kei Moritsugu, Koh Takeuchi, Yoshifumi Fukunishi, and Ikuo Fukuda
    • Organizer
      CBI学会2020大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Coupled Nose-Hoover方程式による温度―エネルギー空間上の高効率サンプリングの実現2020

    • Author(s)
      福田育夫,森次圭,福西快文
    • Organizer
      日本物理学会第75回年次大会
    • Related Report
      2019 Research-status Report
  • [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
      2019 Research-status Report
  • [Presentation] 一般的な摩擦項をもつ運動方程式に対する拡張されたベルレ型積分法2019

    • Author(s)
      福田育夫
    • Organizer
      日本物理学会2019年秋季大会
    • Related Report
      2019 Research-status Report
  • [Presentation] A nonlinear ordinary differential equation with a fully statistical description for a physical system and an environment system2019

    • Author(s)
      Ikuo Fukuda, Kei Moritsugu, Yoshifumi Fukunishi
    • Organizer
      8th International Nonlinear Science Conference 2019
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 温度制御方程式系の合成とその応用可能性2019

    • Author(s)
      福田育夫,森次圭,福西快文
    • Organizer
      日本物理学会第74回年次大会
    • Related Report
      2018 Research-status Report
  • [Presentation] Double density dynamics and coupled Nose-Hoover equations2018

    • Author(s)
      Ikuo Fukuda and Kei Moritsugu
    • Organizer
      The 2nd Global Conference on Applied Physics, Mathematics and Computing
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] A coupling of physical system and a temperature system: Coupled Nose-Hoover equations2018

    • Author(s)
      Ikuo Fukuda and Kei Moritsugu
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Multicopy/multiscale simulations and their applications using massive computing2018

    • Author(s)
      Kei Moritsugu, Tohru Terada, Ryuji Ishida, Akinori Kidera
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] MSES 法によるタンパク質の網羅的構造探索2018

    • Author(s)
      森次圭
    • Organizer
      レア・イベントの計算科学 第2回ワークショップ
    • Related Report
      2018 Research-status Report
  • [Presentation] 合成系密度力学の開発2018

    • Author(s)
      福田育夫,森次圭
    • Organizer
      日本物理学会
    • Related Report
      2017 Research-status Report
  • [Presentation] Non-Ewald method for accurately and efficiently calculating electrostatic interactions in molecular simulations2017

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Han Wang, Shun Sakuraba, Haruki Nakamura
    • Organizer
      “Conformational Ensembles from Experimental Data and Computer Simulations” meeting sponsored by the Biophysical Society
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Non-Ewald methods for simply and precisely calculating electrostatic interactions in molecular simulations2017

    • Author(s)
      Ikuo Fukuda
    • Organizer
      JCUP VIII
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Zero-multipole summation method: non-Ewald method for simply and precisely calculating electrostatic interactions in molecular simulations2017

    • Author(s)
      Ikuo Fukuda
    • Organizer
      Seminar at Science for Life Laboratory, Stockholm University
    • Related Report
      2017 Research-status Report
    • Invited
  • [Book] 長距離力をいかに精度よく効率的に見積もるか―零多重極子和法による静電相互作用計算―2017

    • Author(s)
      福田育夫
    • Total Pages
      7
    • Publisher
      日本物理学会誌
    • Related Report
      2017 Research-status Report

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Published: 2017-04-28   Modified: 2022-01-27  

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