Optimization of Brownian dynamics methods for diffusion‐influenced rate constant calculations
Optimization of Brownian dynamics methods for diffusion‐influenced rate constant calculations
复制标题
用于扩散影响的速率常数计算的布朗动力学方法的优化
DOI：
--
复制
发表时间：
1986
期刊：
影响因子：
--
通讯作者：
J. McCammon
中科院分区：
文献类型：
--
作者：
S. Northrup;M. S. Curvin;S. Allison;J. McCammon
将Lamm和Schulten最近发展的一维布朗反应和反射动力学算法应用于计算三维任意复杂双分子反应扩散影响的速率常数所需的特殊边界拓扑结构。讨论了它们相对于常用的原始自由扩散算法的性能。边界引起的其他误差来源是(1)边界曲率效应和(2)在存在反应取向准则的情况下的反应性不连续效应。这些误差的大小作为模拟时间步长的函数来计算。此外，还开发了一种特殊的统计抽样程序，允许在一次模拟中同时处理一大类反应边界问题。通过处理Solc和Stockmayer模型中反应斑块大小对速率常数的影响，说明了这一过程。
One‐dimensional Brownian dynamics algorithms for reaction and reflection recently developed by Lamm and Schulten are adapted into the special boundary topology necessary to compute diffusion‐influenced rate constants of arbitrarily complicated bimolecular reactions in three dimensions. Performance of these relative to the primitive free diffusion algorithm commonly employed is discussed. Remaining sources of error arising from boundaries are (1) boundary curvature effects and (2) reactive discontinuity effects in cases where orientational criteria for reaction exist. The magnitudes of these errors are calculated as a function of simulation time step size. In addition, a special statistical sampling procedure is developed which allows the simultaneous treatment of a large class of reactive boundary problems in one simulation. This procedure is illustrated by the treatment of reactive patch size effects on the rate constant in the model of Solc and Stockmayer.