Max-Planck-Institute for Developmental Biology, Tübingen, Germany.
Phys Rev Lett. 2012 Sep 7;109(10):100601. doi: 10.1103/PhysRevLett.109.100601. Epub 2012 Sep 4.
Free energy calculations are an important tool in statistical physics and biomolecular simulation. This Letter outlines a Bayesian method to estimate free energies from equilibrium Monte Carlo simulations. A Gibbs sampler is developed that allows efficient sampling of free energies and the density of states. The Gibbs sampling output can be used to estimate expected free energy differences and their uncertainties. The probabilistic formulation offers a unifying framework for existing methods such as the weighted histogram analysis method and the multistate Bennett acceptance ratio; both are shown to be approximate versions of the full probabilistic treatment.
自由能计算是统计物理和生物分子模拟中的重要工具。本文概述了一种从平衡蒙特卡罗模拟中估计自由能的贝叶斯方法。开发了一个 Gibbs 采样器，可有效对自由能和态密度进行采样。Gibbs 采样输出可用于估计预期的自由能差及其不确定性。概率公式为加权直方图分析方法和多态 Bennett 接受比等现有方法提供了统一的框架；两者均被证明是完整概率处理的近似版本。
