Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India.
Center for Computational Science and E-Systems, Japan Atomic Energy Agency, Chiba, Japan.
J Comput Chem. 2021 Oct 30;42(28):1996-2003. doi: 10.1002/jcc.26727. Epub 2021 Aug 16.
Temperature accelerated sliced sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the weighted histogram analysis method (WHAM) which is an iterative post-processing to reweight and stitch high dimensional probability distributions in sliced windows that are obtained in the presence of restraining biases. The WHAM necessitates that TASS windows lie close to each other for proper overlap of distributions and span the collective variable space of interest. On the other hand, increase in number of TASS windows implies more number of simulations, and thus it affects the efficiency of the method. To overcome this problem, we propose herein a new mean-force (MF) based reweighting scheme called TASS-MF, which enables accurate computation with a fewer number of windows devoid of the WHAM post-processing. Application of the technique is demonstrated for alanine di- and tripeptides in vacuo to compute their two- and four-dimensional free energy landscapes, the latter of which is formidable in conventional umbrella sampling and metadynamics. The landscapes are computed within a kcal mol accuracy, ensuring a safe usage for broad applications in computational chemistry.
温度加速切片采样（TASS）是一种计算高维自由能景观的有效方法。原始的 TASS 方法采用加权直方图分析方法（WHAM），这是一种迭代后处理方法，用于对在约束偏置存在下获得的切片窗口中的高维概率分布进行重新加权和拼接。WHAM 要求 TASS 窗口彼此靠近，以便分布的适当重叠并跨越感兴趣的集体变量空间。另一方面，TASS 窗口数量的增加意味着需要更多的模拟，从而影响方法的效率。为了克服这个问题，我们在此提出了一种新的基于平均力（MF）的重新加权方案，称为 TASS-MF，它可以在没有 WHAM 后处理的情况下使用较少的窗口进行准确计算。该技术的应用已通过在真空中对丙氨酸二肽和三肽进行演示，以计算它们的二维和四维自由能景观，后者在传统的伞状采样和元动力学中是艰巨的。景观的计算精度在 kcal/mol 以内，确保在计算化学的广泛应用中安全使用。
