Salvalaglio Matteo, Tiwary Pratyush, Parrinello Michele
Institute of Process Engineering, ETH Zurich , CH-8092 Zurich, Switzerland.
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana , Via G. Buffi 13, 6900 Lugano, Switzerland.
J Chem Theory Comput. 2014 Apr 8;10(4):1420-5. doi: 10.1021/ct500040r. Epub 2014 Mar 10.
Sampling a molecular process characterized by an activation free energy significantly larger than kBT is a well-known challenge in molecular dynamics simulations. In a recent work [Tiwary and Parrinello, Phys. Rev. Lett. 2013, 111, 230602], we have demonstrated that the transition times of activated molecular transformations can be computed from well-tempered metadynamics provided that no bias is deposited in the transition state region and that the set of collective variables chosen to enhance sampling does not display hysteresis. Ensuring though that these two criteria are met may not always be simple. Here we build on the fact that the times of escape from a long-lived metastable state obey Poisson statistics. This allows us to identify quantitative measures of trustworthiness of our calculation. We test our method on a few paradigmatic examples.
在分子动力学模拟中，对一个具有远大于kBT的活化自由能的分子过程进行采样是一个众所周知的挑战。在最近的一项工作中[Tiwary和Parrinello，《物理评论快报》，2013年，第111卷，230602]，我们已经证明，只要在过渡态区域没有偏差沉积，并且为增强采样而选择的一组集体变量不显示滞后现象，活化分子转变的过渡时间就可以从加权元动力学计算出来。然而，确保满足这两个标准并不总是那么简单。在此，我们基于从长寿命亚稳态逃逸的时间服从泊松统计这一事实。这使我们能够确定计算可信度的定量指标。我们在几个典型例子上测试了我们的方法。
