Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
Department of Chemistry, Boston University, Boston, Massachusetts, 02215.
J Comput Chem. 2016 Aug 5;37(21):2017-28. doi: 10.1002/jcc.24430. Epub 2016 Jun 24.
Simulated tempering (ST) is a generalized-ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy landscapes. When implemented using the molecular dynamics method, ST can require the use of short time steps for ensuring the stability of trajectories at high temperatures. To address this shortcoming, a mass-scaling ST (MSST) method is presented in which the particle mass is scaled in proportion to the temperature. Mass scaling in the MSST method leads to velocity distributions that are independent of temperature and eliminates the need for velocity scaling after the accepted temperature updates that are required in conventional ST simulations. The homogeneity in time scales with changing temperature improves the stability of simulations and allows for the use of longer time steps at high temperatures. As a result, the MSST is found to be more efficient than the standard ST method, particularly for cases in which a large temperature range is employed. © 2016 Wiley Periodicals, Inc.
模拟退火（ST）是一种广义系综算法，它采用轨迹探索一系列温度的方法，有效地对崎岖的能量景观进行采样。当使用分子动力学方法实现时，ST 可能需要使用短的时间步长来确保在高温下轨迹的稳定性。为了解决这个缺点，提出了一种质量缩放的 ST（MSST）方法，其中粒子质量与温度成比例地缩放。MSST 方法中的质量缩放导致速度分布与温度无关，并消除了在传统 ST 模拟中所需的接受温度更新后的速度缩放的需要。随温度变化的时间标度的均匀性提高了模拟的稳定性，并允许在高温下使用更长的时间步长。结果表明，MSST 比标准 ST 方法更有效，特别是在使用大温度范围的情况下。© 2016 Wiley Periodicals, Inc.
