Adaptive quantum mechanics/molecular mechanics (QM/MM) reclassifies on-the-fly a molecule or molecular fragment as QM or MM during dynamics simulations without abrupt changes in the energy or forces. Notably, the permuted adaptive-partitioning (PAP) algorithms have been applied to simulate a hydrated proton, with a mobile QM zone anchored at a pseudoatom called a proton indicator. The position of the proton indicator approximates the location of the delocalized excess proton, yielding a smooth trajectory of the proton diffusing via the Grotthuss mechanism in aqueous solutions. The mobile QM zone, which has been taken to be a sphere with a preset radius, follows the proton wherever it goes. Although the simulations are successful, the use of a spherical QM zone has one disadvantage: A large preset radius must be utilized to minimize the chance of missing water molecules that are important to proton translocation. A large radius leads to a large QM zone, which is computationally expensive. In this work, we report a new way to set up the QM zone, where one includes only the water molecules important to proton transfer. The importance of a given water molecule is quantified by its “weight” that depends on its relation to the reaction path of proton transfer. The weight varies smoothly, ensuring that a water molecule gradually appears in or disappears from the QM zone without abrupt changes, as required by the PAP method. Consequently, the shape of the QM zone evolves on-the-fly, keeping the QM zone as small as possible and as large as necessary. Test simulations demonstrate that the new algorithm significantly improves the computation efficiency while maintaining the proper descriptions of proton transfer in bulk water.

中文翻译：

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动态重塑 QM 区域：散装水中水合质子的自适应形状 QM/MM 动态模拟


自适应量子力学/分子力学 (QM/MM) 在动力学模拟过程中将分子或分子片段动态重新分类为 QM 或 MM，而无需能量或力的突然变化。值得注意的是，置换自适应分区（PAP）算法已被应用于模拟水合质子，其中移动 QM 区域锚定在称为质子指示器的伪原子上。质子指示器的位置近似于离域过量质子的位置，从而产生质子通过水溶液中的格罗特胡斯机制扩散的平滑轨迹。移动 QM 区域被视为具有预设半径的球体，无论质子走到哪里，它都会跟随它。尽管模拟是成功的，但使用球形 QM 区域有一个缺点：必须利用较大的预设半径来最大程度地减少丢失对质子易位很重要的水分子的机会。大的半径会导致大的 QM 区域，这在计算上是昂贵的。在这项工作中，我们报告了一种建立 QM 区域的新方法，其中仅包含对质子转移重要的水分子。给定水分子的重要性通过其“重量”来量化，该“重量”取决于其与质子转移反应路径的关系。重量变化平稳，确保水分子逐渐出现在 QM 区域或从 QM 区域消失，而不会突然变化，正如 PAP 方法所要求的那样。因此，QM 区域的形状会动态变化，使 QM 区域尽可能小并根据需要尽可能大。测试模拟表明，新算法显着提高了计算效率，同时保持了对散装水中质子传递的正确描述。