| Item type |
itemtype_ver1(1) |
| 公開日 |
2022-02-08 |
| タイトル |
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|
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
Nagai, Tetsuro
Yamaguchi, Tsuyoshi
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| アクセス権 |
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|
アクセス権 |
open access |
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アクセス権URI |
http://purl.org/coar/access_right/c_abf2 |
| 権利 |
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|
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 |
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|
内容記述タイプ |
Abstract |
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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. |
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言語 |
en |
| 出版者 |
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出版者 |
Wiley |
|
言語 |
en |
| 言語 |
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|
言語 |
eng |
| 資源タイプ |
|
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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 |
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出版タイプResource |
http://purl.org/coar/version/c_ab4af688f83e57aa |
| 関連情報 |
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|
関連タイプ |
isVersionOf |
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|
識別子タイプ |
DOI |
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関連識別子 |
https://doi.org/10.1002/jcc.26742 |
| 収録物識別子 |
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収録物識別子タイプ |
PISSN |
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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
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| ファイル公開日 |
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|
日付 |
2022-11-15 |
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日付タイプ |
Available |
main_R2_ver3.pdf (796 KB)
