论文标题
随机重置以增强采样
Stochastic Resetting for Enhanced Sampling
论文作者
论文摘要
我们提出了一种使用随机重置来增强分子动力学模拟采样的方法。各种现象,从晶体成核到蛋白质折叠的各种现象发生在标准模拟中无法达到的时间尺度上。这通常是由广泛的过渡时间分布引起的,在这种分布中,极慢的事件具有不可忽略的概率。随机重置,即在随机时间重新启动模拟,最近被证明可以显着加快遵循此类分布的过程。在这里,我们首次采用重置来增强分子模拟的采样。我们表明,它可以通过简单模型到分子系统等示例加速长时间的过程。最重要的是,我们以单个重新启动速率从加速模拟中恢复平均过渡时间而不重置的平均过渡时间 - 通常太长而无法直接采样。随机重置可以用作独立方法,也可以与其他采样算法结合使用,以进一步加速模拟。
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations. This is often caused by broad transition time distributions in which extremely slow events have a non-negligible probability. Stochastic resetting, i.e., restarting simulations at random times, was recently shown to significantly expedite processes that follow such distributions. Here, we employ resetting for enhanced sampling of molecular simulations for the first time. We show that it accelerates long-timescale processes by up to an order of magnitude in examples ranging from simple models to molecular systems. Most importantly, we recover the mean transition time without resetting - typically too long to be sampled directly - from accelerated simulations at a single restart rate. Stochastic resetting can be used as a standalone method or combined with other sampling algorithms to further accelerate simulations.