Exploring, Refining, and Validating the Paradynamics QM/MM Sampling
Exploring, Refining, and Validating the Paradynamics QM/MM Sampling
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DOI：
10.1021/jp304678d
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发表时间：
2012-08-30
影响因子：
3.3
通讯作者：
Warshel, Arieh
中科院分区：
文献类型：
--
作者：
Plotnikov, Nikolay V.;Warshel, Arieh
本文研究了在QM/MM计算中的仿射（PD）参考势方法的性能。它还澄清，在对比一些可能的误解，这种方法提供了一个严格的策略QM/MM自由能计算。特别是，PD方法提供了一个渐进的和控制的方式，改善与从EVB参考电位移动到目标QM/MM表面的自由能扰动的评估。这是通过从线性响应近似移动到全自由能微扰方法来评估自由能变化来实现的。我们还提出了一种系统的方法，通过沿着反应坐标使用基于高斯的校正势来提高参考势。同时，我们回顾了其他最近的改编的参考电位的方法，强调和展示的优势，使用EVB电位作为参考电位，相对于半经验QM/MM分子轨道电位。我们还比较PD的结果，通过直接计算的平均力（PMF）的潜力。此外，我们提出了一种加速PMF计算的方法，通过使用基于高斯的负电位沿着反应坐标（这也用于PD细化）。最后，我们讨论了性能的PD和元自洽方法在从头算QM/MM计算，并强调使用PD方法的优势。
The performance of the paradynamics (PD) reference potential approach in QM/MM calculations is examined. It is also clarified that, in contrast to some possible misunderstandings, this approach provides a rigorous strategy for QM/MM free energy calculations. In particular, the PD approach provides a gradual and controlled way of improving the evaluation of the free energy perturbation associated with moving from the EVB reference potential to the target QM/MM surface. This is achieved by moving from the linear response approximation to the full free energy perturbation approach in evaluating the free energy changes. We also present a systematic way of improving the reference potential by using Gaussian-based correction potentials along a reaction coordinate. In parallel, we review other recent adaptations of the reference potential approach, emphasizing and demonstrating the advantage of using the EVB potential as a reference potential, relative to semiempirical QM/MM molecular orbital potentials. We also compare the PD results to those obtained by direct calculations of the potentials of the mean force (PMF). Additionally, we propose a way of accelerating the PMF calculations by using Gaussian-based negative potentials along the reaction coordinate (which are also used in the PD refinement). Finally, we discuss performance of the PD and the metadynamics approaches in ab initio QM/MM calculations and emphasize the advantage of using the PD approach.