Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
J Chem Phys. 2012 Sep 14;137(10):104101. doi: 10.1063/1.4748278.
We introduce an adaptive weighted-ensemble procedure (aWEP) for efficient and accurate evaluation of first-passage rates between states for two-state systems. The basic idea that distinguishes aWEP from conventional weighted-ensemble (WE) methodology is the division of the configuration space into smaller regions and equilibration of the trajectories within each region upon adaptive partitioning of the regions themselves into small grids. The equilibrated conditional∕transition probabilities between each pair of regions lead to the determination of populations of the regions and the first-passage times between regions, which in turn are combined to evaluate the first passage times for the forward and backward transitions between the two states. The application of the procedure to a non-trivial coarse-grained model of a 70-residue calcium binding domain of calmodulin is shown to efficiently yield information on the equilibrium probabilities of the two states as well as their first passage times. Notably, the new procedure is significantly more efficient than the canonical implementation of the WE procedure, and this improvement becomes even more significant at low temperatures.
我们提出了一种自适应加权集合（aWEP）方法，用于高效、准确地评估两态系统中状态间的首次通过速率。aWEP 与传统加权集合（WE）方法的基本区别在于将配置空间划分为较小的区域，并在自适应分区后在每个区域内平衡轨迹。在每个区域对之间的平衡条件/转移概率导致区域的种群和区域之间的首次通过时间的确定，这反过来又组合起来以评估两个状态之间的正向和反向转移的首次通过时间。该程序在钙调蛋白的 70 残基钙结合域的非平凡粗粒化模型中的应用表明，它能够有效地提供关于两个状态的平衡概率及其首次通过时间的信息。值得注意的是，新程序比 WE 程序的标准实现效率更高，而在低温下，这种改进更为显著。
