Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations.
Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations.
复制标题
自适应 QM/MM 模拟中 QM/MM 边界伪影的定量分析和校正。
DOI：
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发表时间：
2019
影响因子：
5.5
通讯作者：
Q. Cui
中科院分区：
文献类型：
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作者：
Hiroshi C. Watanabe;Q. Cui
由于 QM 和 MM 溶剂在 QM 溶质附近进行交换，因此使用标准量子力学/分子力学 (QM/MM) 分子动力学模拟对溶剂化效应进行量子化学处理具有挑战性。为此，人们提出了各种自适应QM/MM方法；根据与 QM 溶质的距离，通过在 QM 和 MM 系统之间灵活切换其身份，可以实现自由溶剂交换。然而，自适应 QM/MM 方法的标准实现中仍然存在时间和空间不连续性，并继续阻碍稳定和准确的动态模拟。我们之前证明了大小一致的多分区（SCMP）方法实现了时间连续性，同时在某种程度上避免了空间不连续性。在本研究中，我们证明残余空间不连续性在某些条件下可能会导致严重的伪影。通过定量分析，我们表明包括 QM/MM 方法在内的所有多尺度方法都可能遇到这些问题，但迄今为止尚未得到深入研究。为了减轻这些伪影，我们在 SCMP 方法的框架中提出了一种校正方案，并使用散装水模拟证明了其有效性。
A quantum chemical treatment of solvation effects using the standard quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations is challenging due to QM and MM solvent exchange near the QM solute. To this end, various adaptive QM/MM methods have been proposed; free solvent exchanges are allowed via flexible switching of their identities between QM and MM systems depending on their distances from the QM solute. However, temporal and spatial discontinuities remain in the standard implementations of adaptive QM/MM approaches and continue to hamper stable and accurate dynamics simulations. We previously demonstrated that the size-consistent multipartitioning (SCMP) method achieves temporal continuity while, to some extent, avoiding spatial discontinuities. In the present study, we demonstrate that residual spatial discontinuities may lead to severe artifacts under certain conditions. Through quantitative analyses, we show that all multiscale including QM/MM methods might experience these problems, which so far have not been investigated in depth. To alleviate these artifacts, we propose a correction scheme in the framework of the SCMP approach and demonstrate its effectiveness using bulk water simulations.
影响因子：
5.5
作者：
Gaus, Michael;Goez, Albrecht;Elstner, Marcus
通讯作者：
Elstner, Marcus