分子体系中多反应途径的快速确定：软棘轮算法
Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm
摘要：
我们讨论了“软棘轮”算法，该算法产生有针对性的随机轨迹在分子系统中的分数对应于他们的概率。该程序，这需要没有初始的路径猜测，是能够快速确定已知状态之间的多个路径。不需要向目标状态的单调进展。将软棘轮算法应用于丙氨酸二肽的全原子模型，假设其无偏轨道遵循过阻尼Langevin动力学。确定了二维二面角曲面上所有可能的路径。相关的概率得分虽然目前不是最优分布的，但是可以提供用于估计反应速率的机制。
英文摘要：
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of rapidly determining multiple pathways between known states. Monotonic progress toward the target state is not required. The soft-ratcheting algorithm is applied to an all-atom model of alanine dipeptide, whose unbiased trajectories are assumed to follow overdamped Langevin dynamics. All possible pathways on the two-dimensional dihedral surface are determined. The associated probability scores, though not optimally distributed at present, may provide a mechanism for estimating reaction rates.
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