Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
J Chem Phys. 2012 Jul 28;137(4):044106. doi: 10.1063/1.4737094.
This work presents a replica exchanging self-guided Langevin dynamics (RXSGLD) simulation method for efficient conformational searching and sampling. Unlike temperature-based replica exchanging simulations, which use high temperatures to accelerate conformational motion, this method uses self-guided Langevin dynamics (SGLD) to enhance conformational searching without the need to elevate temperatures. A RXSGLD simulation includes a series of SGLD simulations, with simulation conditions differing in the guiding effect and/or temperature. These simulation conditions are called stages and the base stage is one with no guiding effect. Replicas of a simulation system are simulated at the stages and are exchanged according to the replica exchanging probability derived from the SGLD partition function. Because SGLD causes less perturbation on conformational distribution than high temperatures, exchanges between SGLD stages have much higher probabilities than those between different temperatures. Therefore, RXSGLD simulations have higher conformational searching ability than temperature based replica exchange simulations. Through three example systems, we demonstrate that RXSGLD can generate target canonical ensemble distribution at the base stage and achieve accelerated conformational searching. Especially for large systems, RXSGLD has remarkable advantages in terms of replica exchange efficiency, conformational searching ability, and system size extensiveness.
本文提出了一种复制交换自导朗之万动力学（RXSGLD）模拟方法，用于高效的构象搜索和采样。与基于温度的复制交换模拟不同，后者使用高温来加速构象运动，而该方法使用自导朗之万动力学（SGLD）来增强构象搜索，而无需升高温度。RXSGLD 模拟包括一系列 SGLD 模拟，模拟条件在引导效果和/或温度上有所不同。这些模拟条件称为阶段，基础阶段是没有引导效果的阶段。模拟系统的副本在这些阶段进行模拟，并根据 SGLD 配分函数导出的复制交换概率进行交换。由于 SGLD 对构象分布的干扰小于高温，因此 SGLD 阶段之间的交换概率远高于不同温度之间的交换概率。因此，RXSGLD 模拟比基于温度的复制交换模拟具有更高的构象搜索能力。通过三个示例系统，我们证明了 RXSGLD 可以在基础阶段生成目标正则系综分布，并实现加速构象搜索。特别是对于大型系统，RXSGLD 在复制交换效率、构象搜索能力和系统大小扩展性方面具有显著优势。
