Finding transition pathways using the string method with swarms of trajectories
Finding transition pathways using the string method with swarms of trajectories
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DOI：
10.1021/jp0777059
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发表时间：
2008-03-20
影响因子：
3.3
通讯作者：
Roux, Benoit
中科院分区：
文献类型：
--
作者：
Pan, Albert C.;Sezer, Deniz;Roux, Benoit
提出了一种在复杂系统中寻找过渡路径的方法。该方法与Maragliano等人（J.Chem.Phys.2006，125，024106）的集合变量中的字符串方法相关，在概念上简单并且易于实现。它包括在多维空间中使用这些变量的平均动态漂移来改进由一组集体变量支持的假定过渡路径。这种漂移估计上的飞行通过成群的短无偏轨迹开始在不同的点沿着的path. Successful迭代的算法，这可以自然地分布在许多计算机节点与可忽略的处理器间的通信，细化两个稳定盆地之间的最可能的过渡路径（MPTP）的初始试验路径。首先测试的方法是通过确定的C-7 eq的C-7ax过渡的全原子模型中的丙氨酸二肽在真空中，这已经研究了以前的字符串方法在集体变量的途径。一个过渡路径被发现与committor分布峰值在1/2附近的自由能最大值，在雅阁与以前的结果。最后，该方法适用于变构构象变化的氮调节蛋白C（NtrC），这里表示与两个状态的弹性网络模型。尽管使用了550多个集合变量来描述构象变化，但路径收敛得很快。再次，commitator分布被发现在两个稳定状态之间的自由能最大值附近的1/2左右达到峰值，证实了一个真正的过渡态已经被定位在这个复杂的多维系统中。
An approach to find transition pathways in complex systems is presented. The method, which is related to the string method in collective variables of Maragliano et al. (J. Chem. Phys. 2006, 125, 024106), is conceptually simple and straightforward to implement. It consists of refining a putative transition path in the multidimensional space supported by a set of collective variables using the average dynamic drift of those variables. This drift is estimated on-the-fly via swarms of short unbiased trajectories started at different points along the path. Successive iterations of this algorithm, which can be naturally distributed over many computer nodes with negligible interprocessor communication, refine an initial trial path toward the most probable transition path (MPTP) between two stable basins. The method is first tested by determining the pathway for the C-7eq to C-7ax transition in an all-atom model of the alanine dipeptide in vacuum, which has been studied previously with the string method in collective variables. A transition path is found with a committor distribution peaked at 1/2 near the free energy maximum, in accord with previous results. Last, the method is applied to the allosteric conformational change in the nitrogen regulatory protein C (NtrC), represented here with a two-state elastic network model. Even though more than 550 collective variables are used to describe the conformational change, the path converges rapidly. Again, the committor distribution is found to be peaked around 1/2 near the free energy maximum between the two stable states, confirming that a genuine transition state has been localized in this complex multidimensional system.