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首页> 外文期刊>Journal of chemical theory and computation: JCTC >Dual Grid Methods for Finding the Reaction Path on Reduced Potential Energy Surfaces
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Dual Grid Methods for Finding the Reaction Path on Reduced Potential Energy Surfaces

机译:在降低的势能面上寻找反应路径的双网格方法

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Two new algorithms are presented for determining the minimum energy reaction path (MEP) on the reduced potential energy surface (RPES) starting with only the reactant. These approaches are based on concepts from the fast marching method (FMM), which expands points outward as a wavefront on a multidimensional grid from the reactant until the product is reached. The MEP is then traced backward to the reactant. Since the number of possible grid points that must be considered grows exponentially with increasing dimensionality of the RPES, interpolation is important for maintaining manageable computational costs. In this work, we use Shepard interpolation, which we have modified to resolve problems in overfitting. In contrast to FMM, which accurately locates the MEP, the new algorithms focus on locating the single rate-limiting transition state and provide only a rough estimate of the MEP. They do this by mapping out the RPES on a coarse grid and then refining a least action path on a finer grid. This is done so that the majority of the interpolation is done on the finer grid, which minimizes the amount of extrapolation inherent in an outward searching algorithm. The first method scans the entire PES before iteratively locating the transition state (TS) for the MEP on the lower bound estimate of the fine PES. The second method explores the coarse grid in a similar manner to FMM and then iteratively locates the rate-limiting TS in the same manner as the first method. Both methods are shown to be capable of rapidly obtaining (in less than 30 constrained optimization cycles) an approximation to the MEP and the rate limiting TS for three example systems: the 4-well potential, the molecule N-hydroxymethyl-methylnitrosaminee (HMMN), and a cluster model of DNA-uracil glycosylase.
机译:提出了两种新算法,用于确定仅从反应物开始的还原势能表面(RPES)上的最小能量反应路径(MEP)。这些方法基于快速前进方法(FMM)的概念,该方法将点作为波阵面从反应物向外扩展成波前,直到到达生成物为止。然后将MEP追溯到反应物。由于必须考虑的可能网格点的数量随RPES尺寸的增加而呈指数增长,因此插值对于保持可管理的计算成本很重要。在这项工作中,我们使用了Shepard插值,我们对其进行了修改以解决过拟合中的问题。与精确定位MEP的FMM相比,新算法着重于定位单个速率限制的过渡状态,并且仅提供MEP的粗略估计。他们通过在粗糙的网格上绘制RPES,然后在更精细的网格上细化最少动作路径来做到这一点。这样做是为了使大部分插值操作都在较细的网格上完成,从而最大程度地减少了向外搜索算法中固有的外推量。第一种方法是在精细PES的下界估计值上迭代定位MEP的过渡状态(TS)之前,扫描整个PES。第二种方法以类似于FMM的方式探索粗糙网格,然后以与第一种方法相同的方式迭代定位限速TS。两种方法均显示出能够快速获得(少于30个约束优化循环)三个示例系统的MEP和速率限制TS的近似值:4孔电势,分子N-羟甲基-甲基亚硝胺(HMMN) ,以及DNA-尿嘧啶糖基化酶的簇模型。

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