Mori Yoshiharu, Okumura Hisashi
Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan.
Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan.
J Comput Chem. 2015 Dec 5;36(31):2344-9. doi: 10.1002/jcc.24213. Epub 2015 Oct 15.
Simulated tempering (ST) is a useful method to enhance sampling of molecular simulations. When ST is used, the Metropolis algorithm, which satisfies the detailed balance condition, is usually applied to calculate the transition probability. Recently, an alternative method that satisfies the global balance condition instead of the detailed balance condition has been proposed by Suwa and Todo. In this study, ST method with the Suwa-Todo algorithm is proposed. Molecular dynamics simulations with ST are performed with three algorithms (the Metropolis, heat bath, and Suwa-Todo algorithms) to calculate the transition probability. Among the three algorithms, the Suwa-Todo algorithm yields the highest acceptance ratio and the shortest autocorrelation time. These suggest that sampling by a ST simulation with the Suwa-Todo algorithm is most efficient. In addition, because the acceptance ratio of the Suwa-Todo algorithm is higher than that of the Metropolis algorithm, the number of temperature states can be reduced by 25% for the Suwa-Todo algorithm when compared with the Metropolis algorithm.
模拟回火(ST)是一种增强分子模拟采样的有用方法。使用ST时,通常应用满足细致平衡条件的Metropolis算法来计算转移概率。最近,Suwa和Todo提出了一种满足全局平衡条件而非细致平衡条件的替代方法。在本研究中,提出了采用Suwa-Todo算法的ST方法。使用三种算法(Metropolis算法、热浴算法和Suwa-Todo算法)进行带ST的分子动力学模拟以计算转移概率。在这三种算法中,Suwa-Todo算法产生最高的接受率和最短的自相关时间。这些表明使用Suwa-Todo算法进行ST模拟采样是最有效的。此外,由于Suwa-Todo算法的接受率高于Metropolis算法,与Metropolis算法相比,Suwa-Todo算法的温度状态数可减少25%。