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arXiv 2206.15366physics.chem-ph
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具有构象依赖分布电荷的分子动力学

Molecular Dynamics with Conformationally Dependent, Distributed Charges

Eric D. Boittier, Mike Devereux, Markus Meuwly

摘要:

在分子模拟中,考虑几何引起的电子分布变化对于捕获电荷流、电荷各向异性和极化等效应非常重要。多极力场已经证明了它们能够定性和正确地表示化学上重要的特征,如σ孔。它还表明,偏离中心的点电荷提供了一个紧凑的替代具有类似的精度。在这里,它表明,允许搬迁的最小分布的电荷模型(MDCM)相对于其参考原子内的电荷是一个可行的路线,以捕捉分子电荷分布的变化取决于几何形状。该方法被称为"柔性MDCM“(fMDCM),在许多小分子上得到验证,与电子结构计算的参考数据相比,静电势(ESP)的平均精度为0.5 kcal/mol,而MDCM和点电荷的均方根误差高出2至5倍。此外,MD模拟中的$NVE$系综使用fMDCM的灵活的水分子与周期性的边界条件的盒子显示了0.1千卡/摩尔的宽度波动的平均值在300 K的10 ns的时间尺度上。在捕捉的ESP的几何形状依赖的准确性,以及在节能模拟的长期稳定性,使fMDCM一个很有前途的工具,引入先进的静电原子模拟。

英文摘要:

Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their ability to qualitatively and correctly represent chemically significant features such as sigma holes. It has also been shown that off-center point charges offer a compact alternative with similar accuracy. Here it is demonstrated that allowing relocation of charges within a minimally distributed charge model (MDCM) with respect to their reference atoms is a viable route to capture changes in the molecular charge distribution depending on geometry. The approach, referred to as ``flexible MDCM'' (fMDCM) is validated on a number of small molecules and provides accuracies in the electrostatic potential (ESP) of 0.5 kcal/mol on average compared with reference data from electronic structure calculations whereas MDCM and point charges have root mean squared errors of a factor of 2 to 5 higher. In addition, MD simulations in the $NVE$ ensemble using fMDCM for a box of flexible water molecules with periodic boundary conditions show a width of 0.1 kcal/mol for the fluctuation around the mean at 300 K on the 10 ns time scale. The accuracy in capturing the geometry dependence of the ESP together with the long-time stability in energy conserving simulations makes fMDCM a promising tool to introduce advanced electrostatics into atomistic simulations.

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