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  1. B200 工学部/工学研究科
  2. B200a 雑誌掲載論文
  3. 学術雑誌

Momentum removal to obtain the position‐dependent diffusion constant in constrained molecular dynamics simulation

http://hdl.handle.net/2237/0002002048
http://hdl.handle.net/2237/0002002048
d0226876-3ce4-4f9e-9ea7-cf9914186be3
名前 / ファイル ライセンス アクション
main_R2_ver3.pdf main_R2_ver3.pdf (796 KB)
Item type itemtype_ver1(1)
公開日 2022-02-08
タイトル
タイトル Momentum removal to obtain the position‐dependent diffusion constant in constrained molecular dynamics simulation
言語 en
著者 Fujimoto, Kazushi

× Fujimoto, Kazushi

en Fujimoto, Kazushi

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Nagai, Tetsuro

× Nagai, Tetsuro

en Nagai, Tetsuro

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Yamaguchi, Tsuyoshi

× Yamaguchi, Tsuyoshi

en Yamaguchi, Tsuyoshi

Search repository
アクセス権
アクセス権 open access
アクセス権URI http://purl.org/coar/access_right/c_abf2
権利
言語 en
権利情報 "This is the peer reviewed version of the following article: [Fujimoto, K., Nagai, T., Yamaguchi, T., J. Comput. Chem. 2021, 42( 30), 2136. https://doi.org/10.1002/jcc.26742], which has been published in final form at [https://doi.org/10.1002/jcc.26742]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited."
内容記述
内容記述 The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink–Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, τv0, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate τv0 value in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf–Roux method.
言語 en
内容記述タイプ Abstract
出版者
言語 en
出版者 Wiley
言語
言語 eng
資源タイプ
資源タイプresource http://purl.org/coar/resource_type/c_6501
タイプ journal article
出版タイプ
出版タイプ AM
出版タイプResource http://purl.org/coar/version/c_ab4af688f83e57aa
関連情報
関連タイプ isVersionOf
識別子タイプ DOI
関連識別子 https://doi.org/10.1002/jcc.26742
収録物識別子
収録物識別子タイプ PISSN
収録物識別子 0192-8651
書誌情報 en : Journal of Computational Chemistry

巻 42, 号 30, p. 2136-2144, 発行日 2021-11-15
ファイル公開日
日付 2022-11-15
日付タイプ Available
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