Fragment molecular orbital method: Application to molecular dynamics simulation, 'ab initio FMO-MD'

Yuto Komeiji; Tatsuya Nakano; Kaori Fukuzawa; Yutaka Ueno; Yuichi Inadomi; Tadashi Nemoto; Masami Uebayasi; Dmitri G. Fedorov; Kazuo Kitaura

doi:10.1016/S0009-2614(03)00430-5

Fragment molecular orbital method: Application to molecular dynamics simulation, 'ab initio FMO-MD'

Yuto Komeiji, Tatsuya Nakano, Kaori Fukuzawa, Yutaka Ueno, Yuichi Inadomi, Tadashi Nemoto, Masami Uebayasi, Dmitri G. Fedorov, Kazuo Kitaura

研究成果: Article › 査読

95 被引用数 (Scopus)

抄録

A quantum molecular simulation method applicable to biological molecules is proposed. Ab initio fragment molecular orbital method-based molecular dynamics (FMO-MD) combines molecular dynamics simulation with the ab initio fragment molecular orbital method. Here, FMO computes the force acting on each atom's nucleus while MD computes the nuclei's time-dependent evolutions. FMO-MD successfully simulated a small polypeptide, demonstrating the method's applicability to biological molecules.

本文言語	English
ページ（範囲）	342-347
ページ数	6
ジャーナル	Chemical Physics Letters
巻	372
号	3-4
DOI	https://doi.org/10.1016/S0009-2614(03)00430-5
出版ステータス	Published - 2003 4月 29
外部発表	はい

ASJC Scopus subject areas

物理学および天文学（全般）
物理化学および理論化学

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10.1016/S0009-2614(03)00430-5

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title = "Fragment molecular orbital method: Application to molecular dynamics simulation, 'ab initio FMO-MD'",

abstract = "A quantum molecular simulation method applicable to biological molecules is proposed. Ab initio fragment molecular orbital method-based molecular dynamics (FMO-MD) combines molecular dynamics simulation with the ab initio fragment molecular orbital method. Here, FMO computes the force acting on each atom's nucleus while MD computes the nuclei's time-dependent evolutions. FMO-MD successfully simulated a small polypeptide, demonstrating the method's applicability to biological molecules.",

author = "Yuto Komeiji and Tatsuya Nakano and Kaori Fukuzawa and Yutaka Ueno and Yuichi Inadomi and Tadashi Nemoto and Masami Uebayasi and Fedorov, {Dmitri G.} and Kazuo Kitaura",

note = "Funding Information: Y. Komeiji is grateful to Dr. Tohru Terada of RIKEN for advice regarding the temperature constraint method. Development of the A binit-mp program has been supported by a grant-in-aid to T. Nakano from the Information-technology Promotion Agency (IPA). We thank Tsukuba Advanced Computing Center (TACC) for computer support. ",

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doi = "10.1016/S0009-2614(03)00430-5",

language = "English",

volume = "372",

pages = "342--347",

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T1 - Fragment molecular orbital method

T2 - Application to molecular dynamics simulation, 'ab initio FMO-MD'

AU - Komeiji, Yuto

AU - Nakano, Tatsuya

AU - Fukuzawa, Kaori

AU - Ueno, Yutaka

AU - Inadomi, Yuichi

AU - Nemoto, Tadashi

AU - Uebayasi, Masami

AU - Fedorov, Dmitri G.

AU - Kitaura, Kazuo

N1 - Funding Information: Y. Komeiji is grateful to Dr. Tohru Terada of RIKEN for advice regarding the temperature constraint method. Development of the A binit-mp program has been supported by a grant-in-aid to T. Nakano from the Information-technology Promotion Agency (IPA). We thank Tsukuba Advanced Computing Center (TACC) for computer support.

PY - 2003/4/29

Y1 - 2003/4/29

N2 - A quantum molecular simulation method applicable to biological molecules is proposed. Ab initio fragment molecular orbital method-based molecular dynamics (FMO-MD) combines molecular dynamics simulation with the ab initio fragment molecular orbital method. Here, FMO computes the force acting on each atom's nucleus while MD computes the nuclei's time-dependent evolutions. FMO-MD successfully simulated a small polypeptide, demonstrating the method's applicability to biological molecules.

AB - A quantum molecular simulation method applicable to biological molecules is proposed. Ab initio fragment molecular orbital method-based molecular dynamics (FMO-MD) combines molecular dynamics simulation with the ab initio fragment molecular orbital method. Here, FMO computes the force acting on each atom's nucleus while MD computes the nuclei's time-dependent evolutions. FMO-MD successfully simulated a small polypeptide, demonstrating the method's applicability to biological molecules.

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DO - 10.1016/S0009-2614(03)00430-5

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JO - Chemical Physics Letters

JF - Chemical Physics Letters

SN - 0009-2614

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Fragment molecular orbital method: Application to molecular dynamics simulation, 'ab initio FMO-MD'

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