Finding Transition Pathways Using the String Method with Swarms of Trajectories
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- 作者：Albert C. Pan ; Deniz Sezer ; Benoî ; t Roux
- 刊名：Journal of Physical Chemistry B
- 出版年：2008
- 出版时间：March 20, 2008
- 年：2008
- 卷：112
- 期：11
- 页码：3432 - 3440
- 全文大小：291K
- 年卷期：v.112,no.11(March 20, 2008)
- ISSN：1520-5207
文摘
An approach to find transition pathways in complex systems is presented. The method, which is related tothe string method in collective variables of Maragliano et al. (J. Chem. Phys. 2006, 125, 024106), is conceptuallysimple and straightforward to implement. It consists of refining a putative transition path in the multidimensionalspace supported by a set of collective variables using the average dynamic drift of those variables. This driftis 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 withnegligible 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 C7eq to C7axtransition in an all-atom model of the alanine dipeptide in vacuum, which has been studied previously withthe string method in collective variables. A transition path is found with a committor distribution peaked at1/2 near the free energy maximum, in accord with previous results. Last, the method is applied to the allostericconformational change in the nitrogen regulatory protein C (NtrC), represented here with a two-state elasticnetwork model. Even though more than 550 collective variables are used to describe the conformationalchange, the path converges rapidly. Again, the committor distribution is found to be peaked around 1/2 nearthe free energy maximum between the two stable states, confirming that a genuine transition state has beenlocalized in this complex multidimensional system.