Paper Citing NAMD - Abstract
Mori, Yoshiharu; Okumura, Hisashi
Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:2344-2349, DEC 5 2015
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. (c) 2015 Wiley Periodicals, Inc.
