WEKO3
アイテム
Feasibility of combining biomolecular conformational sampling techniques for molecular dynamics simulation
https://repo.qst.go.jp/records/2001782
https://repo.qst.go.jp/records/2001782c2d0d13e-cc3a-46f2-92b9-7a6fe7907d26
| アイテムタイプ | 学術雑誌論文 / Journal Article(1) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 公開日 | 2025-08-05 | |||||||||||
| タイトル | ||||||||||||
| タイトル | Feasibility of combining biomolecular conformational sampling techniques for molecular dynamics simulation | |||||||||||
| 言語 | en | |||||||||||
| 言語 | ||||||||||||
| 言語 | eng | |||||||||||
| 資源タイプ | ||||||||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||||||||
| 資源タイプ | journal article | |||||||||||
| 著者 |
Ikebe
× Ikebe
× Jinzen
× Kono Hidetoshi
|
|||||||||||
| 抄録 | ||||||||||||
| 内容記述タイプ | Abstract | |||||||||||
| 内容記述 | We assess the feasibility of combining two advanced molecular dynamics techniques for efficient biomolecular conformational sampling: the generalized ensemble method for enhancing conformational sampling in partial systems (GEPS), such as ALSD and REST2, which dynamically modulate atomic charges in selected regions, and the zero-multipole summation method (ZMM), which efficiently computes electrostatic interactions assuming local electrostatic neutrality. To address whether charge variation in GEPS violates the fundamental assumption of ZMM, we compared conformational ensembles obtained using GEPS combined with either ZMM or a conventional electrostatic calculation method. Our results demonstrate that GEPS and ZMM can be effectively combined without introducing systematic bias. Additionally, we identified a potential limitation of ZMM: in highly polarized systems, it may fail to capture long-range electrostatic repulsion, potentially leading to artifacts. These findings support the practical use of GEPS with ZMM for conformational sampling; however, caution is warranted when applying ZMM to systems with highly delocalized electrostatics. | |||||||||||
| 書誌情報 |
Journal of Computational Chemistry 巻 46, 号 20, p. e70192, 発行日 2025-07 |
|||||||||||
| DOI | ||||||||||||
| 識別子タイプ | DOI | |||||||||||
| 関連識別子 | 10.1002/jcc.70192 | |||||||||||
