Automatic method for identifying reaction coordinates in complex systems
Automatic method for identifying reaction coordinates in complex systems
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DOI：
10.1021/jp045546c
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发表时间：
2005-04-14
影响因子：
3.3
通讯作者：
Dinner, AR
中科院分区：
文献类型：
--
作者：
Ma, A;Dinner, AR
为了解释复杂系统的模拟，以确定动力学过程的物理机制，有必要确定区分稳定状态和过渡状态的少量坐标。我们开发了一个自动的方法来识别这些自由度的候选物理变量的数据库。在该方法中，神经网络用于确定提交到一组坐标上的稳定状态（提交者）的概率的函数依赖性，并且遗传算法选择产生最佳拟合的输入的组合。该方法使我们能够获得第一组坐标，其证明足以指定在明确的水分子存在下丙氨酸二肽的C-7 eq-> alpha（R）异构化的过渡态。据透露，溶质-溶剂耦合可以描述由溶剂衍生的静电扭矩周围的主链键之一，和集体，长程性质的这种相互作用占以前的失败，以表征该反应。
To interpret simulations of a complex system to determine the physical mechanism of a dynamical process, it is necessary to identify the small number of coordinates that distinguish the stable states from the transition states. We develop an automatic method for identifying these degrees of freedom from a database of candidate physical variables. In the method neural networks are used to determine the functional dependence of the probability of committing to a stable state (committor) on a set of coordinates, and a genetic algorithm selects the combination of inputs that yields the best fit. The method enables us to obtain the first set of coordinates that is demonstrably sufficient to specify the transition state of the C-7eq -> alpha(R) isomerization of the alanine dipeptide in the presence of explicit water molecules. It is revealed that the solute-solvent coupling can be described by a solvent-derived electrostatic torque around one of the main-chain bonds, and the collective, long-ranged nature of this interaction accounts for previous failures to characterize this reaction.