Usefulness of higher-order system-size correction for macromolecule diffusion coefficients: A molecular dynamics study

被引：1

作者：

Iwashita, Tomoya ^{[1
]}

Nagao, Masaaki ^{[1
]}

Yoshimori, Akira ^{[2
]}

Terazima, Masahide ^{[3
]}

Akiyama, Ryo ^{[1
]}

机构：

[1] Kyushu Univ, Dept Chem, Fukuoka 8120395, Japan

[2] Niigata Univ, Dept Phys, Niigata 9502181, Japan

[3] Kyoto Univ, Dept Chem, Kyoto 6068502, Japan

来源：

CHEMICAL PHYSICS LETTERS | 2022年 / 807卷

基金：

日本学术振兴会;

关键词：

Diffusion coefficient; Effective viscosity; System-size dependence; Protein; Molecular dynamics simulation; CONFORMATIONAL-CHANGES; LINKER; DEPENDENCE; PARTICLE; REGION; SENSOR; LOV2;

D O I：

10.1016/j.cplett.2022.140096

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Yeh and Hummer's simplified estimation method has often been adopted to obtain diffusion coefficients for solute molecules using molecular dynamic simulation. However, the simplified formula is not necessarily valid when a small basic cell is used. Therefore, we conducted molecular dynamics simulations of aqueous protein solution to estimate the diffusion coefficient for the infinite dilution limit. We confirmed a deviation from the simplified formula in the simulation data and rationalized the discrepancy based on the unsimplified formula.

引用

页数：7

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