通过拟合程序降低评估反应坐标的成本。
Reducing the cost of evaluating the committor by a fitting procedure.
作者信息
Li Wenjin, Ma Ao
机构信息
Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan St., Chicago, Illinois 60607, USA.
出版信息
J Chem Phys. 2015 Nov 7;143(17):174103. doi: 10.1063/1.4934782.
Correct identification of reaction coordinates in complex systems is essential for understanding the mechanisms of their reaction dynamics. Existing methods for identifying reaction coordinates typically require knowledge of the committor--the probability of a given configuration to reach the product basin. The high computational cost of evaluating committors has limited applications of methods for identifying reaction coordinates. We proposed a fitting procedure that can reduce the cost of evaluating committors by an order of magnitude or more. The method only requires evaluating the committors of a few configurations in a transition path by the standard and costly shooting procedure. The committors of the other configurations are then estimated with great accuracy by a sigmoid function derived from fitting the few numerically evaluated committors. The method has been systematically tested on a model system of a Brownian particle moving in a one-dimensional double-well potential, and a small biomolecular system--the isomerization of alanine dipeptide in vacuum and in explicit water.
正确识别复杂系统中的反应坐标对于理解其反应动力学机制至关重要。现有的识别反应坐标的方法通常需要知道反应几率——给定构型到达产物盆地的概率。评估反应几率的高计算成本限制了反应坐标识别方法的应用。我们提出了一种拟合程序，该程序可以将评估反应几率的成本降低一个数量级或更多。该方法只需要通过标准且昂贵的打靶程序来评估过渡路径中少数构型的反应几率。然后，通过对少数数值评估的反应几率进行拟合得到的 sigmoid 函数，非常准确地估计其他构型的反应几率。该方法已在一个布朗粒子在一维双阱势中移动的模型系统以及一个小生物分子系统——丙氨酸二肽在真空和显式水中的异构化系统上进行了系统测试。
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