Department of Physics, Nippon Medical School, Nakahara, Kawasaki 211-0063, Japan.
J Chem Phys. 2013 Aug 7;139(5):054117. doi: 10.1063/1.4817209.
We propose a novel path sampling method based on the Onsager-Machlup (OM) action by generalizing the multiscale enhanced sampling technique suggested by Moritsugu and co-workers [J. Chem. Phys. 133, 224105 (2010)]. The basic idea of this method is that the system we want to study (for example, some molecular system described by molecular mechanics) is coupled to a coarse-grained (CG) system, which can move more quickly and can be computed more efficiently than the original system. We simulate this combined system (original + CG system) using Langevin dynamics where different heat baths are coupled to the two systems. When the coupling is strong enough, the original system is guided by the CG system, and is able to sample the configuration and path space with more efficiency. We need to correct the bias caused by the coupling, however, by employing the Hamiltonian replica exchange, where we prepare many path replicas with different coupling strengths. As a result, an unbiased path ensemble for the original system can be found in the weakest coupling path ensemble. This strategy is easily implemented because a weight for a path calculated by the OM action is formally the same as the Boltzmann weight if we properly define the path "Hamiltonian." We apply this method to a model polymer with Asakura-Oosawa interaction, and compare the results with the conventional transition path sampling method.
我们提出了一种基于 Onsager-Machlup (OM) 作用的新路径采样方法，该方法通过推广 Moritsugu 等人提出的多尺度增强采样技术[J. Chem. Phys. 133, 224105 (2010)]。该方法的基本思想是，我们要研究的系统（例如，由分子力学描述的某些分子系统）与粗粒化（CG）系统耦合，后者比原始系统移动更快且计算效率更高。我们使用朗之万动力学模拟这个组合系统（原始+CG 系统），其中不同的热浴与两个系统耦合。当耦合足够强时，原始系统由 CG 系统引导，能够更有效地采样构型和路径空间。然而，我们需要通过采用哈密顿 replica 交换来修正由耦合引起的偏差，其中我们准备了具有不同耦合强度的许多路径副本。结果，在最弱耦合路径集合中可以找到原始系统的无偏路径集合。由于在适当定义路径“哈密顿量”的情况下，由 OM 作用计算的路径的权重在形式上与玻尔兹曼权重相同，因此这种策略很容易实现。我们将该方法应用于具有 Asakura-Oosawa 相互作用的模型聚合物，并将结果与传统的跃迁路径采样方法进行比较。
