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通过分布方法精确计算自由能差。

Accurate calculations of free-energy differences by the distribution method.

作者信息

Wu Di

机构信息

Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China.

出版信息

J Chem Phys. 2008 Jun 14;128(22):224105. doi: 10.1063/1.2936987.

Abstract

We employ the strategy used in the successive umbrella sampling method [P. Virnau and M. Muller, J. Chem. Phys. 120, 10925 (2004)] to obtain the energy-difference distribution over its desired range. This is very helpful in calculating free-energy differences, where the source of the error is well recognized as the insufficient sampling over the relevant tail region in the energy-difference distribution. The distribution method proposed here employs the idea of restricting the sampling within an appropriate energy range, as was presented by Shing and Gubbins in their restricted umbrella sampling method [Mol. Phys. 46, 1109 (1982)]. We demonstrate the efficiency of the distribution method by calculating the free-energy difference of a model of harmonic oscillators where the systems exhibit nonoverlap features in their important phase spaces through the original Metropolis sampling. For this particular case, we show that the distribution method outperforms the free-energy perturbation method and even the Bennett's acceptance ratio method [J. Comput. Phys. 22, 245 (1976)] with the fastest convergence and the smallest relative errors. We further demonstrate the application of the distribution method with a simple point charge water model.

摘要

我们采用连续伞形抽样方法[P. 维尔瑙和M. 米勒,《化学物理杂志》120, 10925 (2004)]中使用的策略,以获得其所需范围内的能量差分布。这在计算自由能差时非常有帮助,在自由能差计算中,误差来源被公认为是能量差分布中相关尾部区域的采样不足。这里提出的分布方法采用了在适当能量范围内限制采样的思想,正如辛和古宾斯在他们的受限伞形抽样方法[《分子物理学》46, 1109 (1982)]中所提出的那样。我们通过计算一个谐振子模型的自由能差来证明分布方法的效率,在这个模型中,系统通过原始的 metropolis 抽样在其重要相空间中呈现出非重叠特征。对于这个特定情况,我们表明分布方法优于自由能微扰方法,甚至优于贝内特接受率方法[《计算物理杂志》22, 245 (1976)],具有最快的收敛速度和最小的相对误差。我们进一步用一个简单的点电荷水模型展示了分布方法的应用。

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