An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates
An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates
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DOI：
10.1063/1.4748278
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发表时间：
2012-09-14
影响因子：
4.4
通讯作者：
Bahar, Ivet
中科院分区：
文献类型：
--
作者：
Bhatt, Divesh;Bahar, Ivet
我们引入了一个自适应加权集成过程（aWEP）的两状态系统的状态之间的首次通过率的有效和准确的评估。区分aWEP从传统的加权合奏（WE）方法的基本思想是配置空间划分成较小的区域和平衡的轨迹在每个区域内的自适应分区的区域本身成小网格。每对区域之间的平衡条件/转移概率导致确定区域的群体和区域之间的第一次通过时间，这又被组合以评估两个状态之间的前向和后向转移的第一次通过时间。该程序的应用程序的一个非平凡的粗粒度模型的70个残基的钙结合域的钙调素有效地产生信息的平衡概率的两个状态，以及它们的第一次通过时间。值得注意的是，新的程序是显着更有效的比规范的实施的WE程序，这种改进在低温下变得更加显着。(C)2012年美国物理学会。[http：//dx.doi.org/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. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4748278]