Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122, United States.
Sci Rep. 2019 Feb 26;9(1):2803. doi: 10.1038/s41598-019-39420-x.
We introduce the UWHAM (binless weighted histogram analysis method) and SWHAM (stochastic UWHAM) software package that can be used to estimate the density of states and free energy differences based on the data generated by multi-state simulations. The programs used to solve the UWHAM equations are written in the C++ language and operated via the command line interface. In this paper, first we review the theoretical bases of UWHAM, its stochastic solver RE-SWHAM (replica exchange-like SWHAM)and ST-SWHAM (serial tempering-like SWHAM). Then we provide a tutorial with examples that explains how to apply the UWHAM program package to analyze the data generated by different types of multi-state simulations: umbrella sampling, replica exchange, free energy perturbation simulations, etc. The tutorial examples also show that the UWHAM equations can be solved stochastically by applying the RE-SWHAM and ST-SWHAM programs when the data ensemble is large. If the simulations at some states are far from equilibrium, the Stratified RE-SWHAM program can be applied to obtain the equilibrium distribution of the state of interest. All the source codes and the tutorial examples are available from our group's web page: https://ronlevygroup.cst.temple.edu/software/UWHAM_and_SWHAM_webpage/index.html .
我们介绍了 UWHAM（无 bin 加权直方图分析方法）和 SWHAM（随机 UWHAM）软件包，可用于根据多态模拟生成的数据估计态密度和自由能差异。用于求解 UWHAM 方程的程序是用 C++语言编写的，并通过命令行界面操作。在本文中，我们首先回顾了 UWHAM 的理论基础、它的随机求解器 RE-SWHAM（类似于 replica exchange 的 SWHAM）和 ST-SWHAM（类似于 serial tempering 的 SWHAM）。然后，我们提供了一个带有示例的教程，解释了如何将 UWHAM 程序包应用于分析来自不同类型的多态模拟的数据：伞状采样、replica exchange、自由能微扰模拟等。该教程示例还表明，当数据集合较大时，可以通过应用 RE-SWHAM 和 ST-SWHAM 程序来随机求解 UWHAM 方程。如果某些状态下的模拟远未达到平衡，可以应用分层 RE-SWHAM 程序来获得感兴趣状态的平衡分布。所有的源代码和教程示例都可以在我们小组的网页上获得：https://ronlevygroup.cst.temple.edu/software/UWHAM_and_SWHAM_webpage/index.html。
