研究者詳細 - 篠田　渉

MISC - 篠田　渉

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水の比熱:経路積分分子動力学法による研究

篠田渉, 志賀基之

分子シミュレーション討論会講演要旨集 18th 2004年

Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency

W Shinoda, M Mikami

JOURNAL OF COMPUTATIONAL CHEMISTRY 24 ( 8 ) 920 - 930 2003年6月

記述言語：英語出版者・発行元：JOHN WILEY & SONS INC

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermalisobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL. (C) 2003 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.10249

分子動力学法による温度とストレスの制御とその応用

志賀基之, 篠田渉, 三上益弘, 蕪木英雄

分子構造総合討論会講演要旨集(CD-ROM) 2003 2003年

大規模系のための汎用分子動力学統合システムTACPACK2000の開発その3 システム化技術

南多善, 森川良忠, 小川浩, 田中真悟, 寺倉清之, 増田裕寿, 三井崇志, 佐々木幹夫, 三上益弘, 篠田渉, 劉子敬, 川田正晃, 池庄司民夫

情報化学討論会講演要旨集 0 ( 0 ) J25 - J25 2001年

出版者・発行元：公益社団法人日本化学会・情報化学部会

The TACPACK2000 system consists of general purpose molecular dynamics simulators for large scale system of complicated materials such as biopolymer, organic crystal, liquid crystal, polymers, semiconductor, metal and alloy and ceramics and integration system for the simulators. In this presentation, the systematization technologies of the integration system are described. In the database management technology, we have developed the new technology using XML(eXtensible Markup Language) to control uniformly the data composed of molecular structure, crystal structure , potential and pseudopotential function etc. Also in the plug-in function, we have developed the software technologies for program restoration / deletion function to this system, compilation linkage functions of the program and automatic generation function of parameters input screen.

DOI： 10.11547/ciqs2001.tokusi.0.J25.0

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分子動力学シミュレーションによる脂質二重層膜の構造と動力学

篠田渉, 岡崎進

電気化学および工業物理化学 : denki kagaku 68 ( 2 ) 129 - 133 2000年2月

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