著者

松井 亨 喜屋武 茜 庄司 光男 重田 育照

出版者

日本コンピュータ化学会

雑誌

Journal of Computer Chemistry, Japan (ISSN:13471767)

巻号頁・発行日

vol.15, no.5, pp.184-191, 2016 (Released:2016-12-27)

参考文献数

37

被引用文献数

1 2

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本総説では,分極誘電体モデルと量子化学計算に基づく酸解離定数(pKa)の計算手法について述べる.この手法では,参照分子に対して計算により得られる自由エネルギー差と実験により得られるpKa値から官能基毎の線形関係を導くことで,アミノ酸の側鎖のpKaの半定量的な計算が可能になる.ペプチド3量体の計算においては,周囲のアミノ酸の水素結合の効果によってpKaが単量体とくらべ大きく(3 pKa単位)異なることがわかる.また本手法は標準水素電極電位の計算にも適用可能であり,いくつかの酸化還元反応の誤差はCCSD (T)/aug-cc-pVDZでは0.1V以内であり,B3LYPでも同程度の精度で酸化還元電位が計算される.

著者

梅田 宏明 塙 敏博 庄司 光男 朴 泰祐 重田 育照

出版者

日本コンピュータ化学会

雑誌

Journal of Computer Chemistry, Japan (ISSN:13471767)

巻号頁・発行日

vol.14, no.3, pp.69-70, 2015 (Released:2015-09-25)

参考文献数

6

被引用文献数

5

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GPU acceleration of four-center (4C) inter-fragment Coulomb interaction term (IFC) for OpenFMO, a fragment molecular orbital calculation program, has been implemented and its performance was examined. FMO calculation has two time-consuming steps: Fock matrix construction and IFC calculation, and in our previous letter, it was reported that the former is successfully accelerated with our GPU-enable code. The 4C-IFC calculation is the core part of the latter and its code is similar to that of Fock matrix construction. In this letter, we briefly describe the GPU-accelerated 4C-IFC calculation routine, and report a performance benchmark for GPU-accelerated FMO calculation. The GPU-accelerated program shows 3.3× speedups from CPU only FMO-HF/6-31G (d) calculation for 642 atomic protein on 8 nodes of HA-PACS base cluster.

著者

原田 隆平 Vladimir Sladek 重田 育照

出版者

日本コンピュータ化学会

雑誌

Journal of Computer Chemistry, Japan (ISSN:13471767)

巻号頁・発行日

vol.18, no.5, pp.199-201, 2019 (Released:2020-02-26)

参考文献数

7

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Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is a rare event sampling method of proteins, which does not rely on knowledge of the target structure. nt-PaCS-MD is an extension of targeted PaCS-MD (t-PaCS-MD). In nt-PaCS-MD, it makes use of cyclic resampling from some relevant initial structures to expand the searched conformational subspace. Reliable identification of these initial structures is the key to using nt-PaCS-MD. In the present study, we introduce the moving root-mean-square deviation (mRMSD) as a metric for identification of these statistical conformation outliers. mRMSD can be calculated for any ith geometry in the trajectory generated by short MD runs. The reference to which the mRMSD relates is the close surrounding of the ith conformation, often the (i-1) st one. Based on mRMSD, we show that it increases its effectiveness compared to the conventional MD.

著者

庄司 光男 磯部 寛 重田 育照 中嶋 隆人 山口 兆

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.58, no.3, pp.127-133, 2018 (Released:2018-05-31)

参考文献数

30

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Photosystems are natural energy conversion systems evolved for over 2,700 million years. Among the photosystems, photosystem II (PSII) catalyzes the light-driven water decomposition reaction with the production of O2, protons and electrons to reduce plastoquinone. The reaction is important not only for understanding natural photosynthesis but also for creating efficient artificial photosynthesis. In this review, PSII catalytic intermediate states and their reaction mechanisms elucidated by experimental and theoretical approaches are introduced mainly following the development of the X-ray crystallography. For the O2 formation mechanism, two representative mechanisms, acid-base and radical coupling, are explained. Finally, we discuss the geometrical and electronic structures of inorganic model complex in comparison with those of the native catalytic center in PSII.

著者

馬場 剛史 安東 寛之 重田 育照

出版者

分子シミュレーション研究会

雑誌

アンサンブル (ISSN:18846750)

巻号頁・発行日

vol.16, no.1, pp.36-41, 2014

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溶液中や酵素などの大自由度系の化学反応において,自由エネルギーの計算は非常に重要である.本解説では熱力学積分法に基づくブルームーンアンサンブル法,および,ヒューリスティックな方法では有るが非常に強力な研究手段であるメタダイナミクス法について説明し,SN2 反応や酵素反応での応用例を示す.