论文标题
部分可观测时空混沌系统的无模型预测
Enhanced path sampling using subtrajectory Monte Carlo moves
论文作者
论文摘要
路径采样可以研究罕见事件,例如化学反应,成核和蛋白质通过路径空间中的蒙特卡洛(MC)探索。该方法不是配置点,而不是配置点,以特定的起始条件和终端条件采样了短分子动力学(MD)轨迹。与配置MC一样,它的效率在很大程度上取决于MC移动的类型。自过去二十年以来,中央MC进行采样的中央移动是所谓的射击动作,在该动作中,旧路径的扰动相位点被及时向后传播,以产生新的路径。最近,我们提出了子三号动作,石材鞋底(SS)和网络投入(WT),这些动作显然更有效。但是,一步交叉要求使它们结合外部MD程序或订单参数确定昂贵时更难实施。在本文中,我们提出了解决该问题的策略。最通用的解决方案是子三射移动的新成员,电线围栏(WF),比SS少,但更通用。这使得将路径采样代码与外部MD软件包链接起来变得更加容易,并为计算订单参数计算昂贵或不是几何函数的情况提供了一个实用的解决方案。我们在双井模型中演示了WF移动,基于经典力场的薄膜破裂过渡,以及在从头静止水平上的较小的ruthenium氧化还原反应,其中顺序参数明确取决于电子密度。
Path sampling allows the study of rare events like chemical reactions, nucleation and protein folding via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short molecular dynamics (MD) trajectories with specific start- and end-conditions. As in configuration MC, its efficiency highly depends on the types of MC moves. Since the last two decades, the central MC move for path sampling has been the so-called shooting move in which a perturbed phase point of the old path is propagated backward and forward in time to generate a new path. Recently, we proposed the subtrajectory moves, stone-skipping (SS) and web-throwing (WT), that are demonstrably more efficient. However, the one-step crossing requirement makes them somewhat more difficult to implement in combination with external MD programs or when the order parameter determination is expensive. In this article, we present strategies to address the issue. The most generic solution is a new member of subtrajectory moves, wire fencing (WF), that is less thrifty than the SS, but more versatile. This makes it easier to link path sampling codes with external MD packages and provides a practical solution for cases where the calculation of the order parameter is expensive or not a simple function of geometry. We demonstrate the WF move in a double well Langevin model, a thin film breaking transition based on classical force fields, and a smaller ruthenium redox reaction at the ab initio level in which the order parameter explicitly depends on the electron density.