Biomolecular Physics and Modelling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
J Comput Chem. 2016 Jun 30;37(17):1565-75. doi: 10.1002/jcc.24371. Epub 2016 Apr 5.
Replica Exchange Molecular Dynamics (REMD) method is a powerful sampling tool in molecular simulations. Recently, we made a modification to the standard REMD method. It places some inactive replicas at different temperatures as well as the active replicas. The method completely decouples the number of the active replicas and the number of the temperature levels. In this article, we make a further modification to our previous method. It uses the inactive replicas in a different way. The inactive replicas first sample in their own knowledge-based energy databases and then participate in the replica exchange operations in the REMD simulation. In fact, this method is a hybrid between the standard REMD method and the simulated tempering method. Using different active replicas, one can freely control the calculation quantity and the convergence speed of the simulation. To illustrate the performance of the method, we apply it to some small models. The distribution functions of the replicas in the energy space and temperature space show that the modified REMD method in this work can let the replicas walk freely in both of the two spaces. With the same number of the active replicas, the free energy surface in the simulation converges faster than the standard REMD. © 2016 Wiley Periodicals, Inc.
复制交换分子动力学 (REMD) 方法是分子模拟中一种强大的采样工具。最近，我们对标准 REMD 方法进行了修改。它在不同温度下放置一些非活性副本以及活性副本。该方法完全分离了活性副本的数量和温度水平的数量。在本文中，我们对之前的方法进行了进一步的修改。它以不同的方式使用非活性副本。非活性副本首先在自己的基于知识的能量数据库中进行采样，然后参与 REMD 模拟中的副本交换操作。实际上，该方法是标准 REMD 方法和模拟淬火方法的混合体。使用不同的活性副本，人们可以自由控制模拟的计算量和收敛速度。为了说明该方法的性能，我们将其应用于一些小模型。在能量空间和温度空间中，副本的分布函数表明，本文中的改进的 REMD 方法可以使副本在这两个空间中自由移动。使用相同数量的活性副本，模拟中的自由能表面收敛速度比标准 REMD 更快。© 2016 威利父子公司
