ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS.
ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS.
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DOI：
10.1051/proc/201448009
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发表时间：
2015-01-01
期刊：
影响因子：
--
通讯作者：
Teo, Ivan
中科院分区：
文献类型：
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作者：
Aristoff, David;Lelievre, Tony;Teo, Ivan
自适应多级分裂 (AMS) 是一种基于副本的稀有事件采样方法，已成功用于高维随机模拟，以识别跨越将一个亚稳态与另一个亚稳态分开的高势垒的轨迹，并估计观察到此类轨迹的概率。 AMS 的一个吸引人的特点是，在大量副本的限制下，无论选择何种反应坐标来表征轨迹，它仍然有效。之前的研究表明 AMS 在蒙特卡罗模拟中是准确的。在这项研究中，我们将 AMS 的应用扩展到分子动力学模拟，并使用简单的测试系统证明了其有效性。我们的结论为有用的应用铺平了道路，例如药物从蛋白质靶标解离的特征时间的分子动力学计算。
Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target.