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Momentum removal to obtain the position-dependent diffusion constant in constrained molecular dynamics simulation
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2021-08-18 , DOI: 10.1002/jcc.26742 Kazushi Fujimoto 1 , Tetsuro Nagai 2 , Tsuyoshi Yamaguchi 3
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2021-08-18 , DOI: 10.1002/jcc.26742 Kazushi Fujimoto 1 , Tetsuro Nagai 2 , Tsuyoshi Yamaguchi 3
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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, 
, 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 
value in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf–Roux method.
中文翻译：
在约束分子动力学模拟中去除动量以获得位置相关的扩散常数
与位置相关的扩散系数和自由能分布是研究生物和聚合物膜等异质系统中的质量传输所需的重要参数，而分子动力学 (MD) 计算是获得它们的常用工具。在众多方法中，通常采用 Marrink-Berendsen (MB) 方法来计算位置相关的扩散系数，其中固定分子上的力的自相关函数与分子上的摩擦有关。然而，扩散系数显示受质心速度去除周期的影响，，在使用 Ewald 方法进行库仑相互作用进行 MD 计算时，这是必需的。我们在本研究中从理论上阐明了该操作如何影响 MB 方法计算的扩散系数，并通过 MD 计算证明了理论预测。因此，我们成功地指导了如何在 MB 方法估计位置相关扩散系数时选择合适的值。本指南也适用于 Woolf-Roux 方法。
更新日期：2021-10-09
, 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 value in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf–Roux method.
中文翻译：
在约束分子动力学模拟中去除动量以获得位置相关的扩散常数
与位置相关的扩散系数和自由能分布是研究生物和聚合物膜等异质系统中的质量传输所需的重要参数，而分子动力学 (MD) 计算是获得它们的常用工具。在众多方法中，通常采用 Marrink-Berendsen (MB) 方法来计算位置相关的扩散系数，其中固定分子上的力的自相关函数与分子上的摩擦有关。然而，扩散系数显示受质心速度去除周期的影响，
，在使用 Ewald 方法进行库仑相互作用进行 MD 计算时，这是必需的。我们在本研究中从理论上阐明了该操作如何影响 MB 方法计算的扩散系数，并通过 MD 计算证明了理论预测。因此，我们成功地指导了如何在 MB 方法估计位置相关扩散系数时选择合适的值。本指南也适用于 Woolf-Roux 方法。
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