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Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2021-08-16 , DOI: 10.1002/jcc.26727 Asit Pal 1 , Subhendu Pal 1 , Shivani Verma 1 , Motoyuki Shiga 2 , Nisanth N Nair 1
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2021-08-16 , DOI: 10.1002/jcc.26727 Asit Pal 1 , Subhendu Pal 1 , Shivani Verma 1 , Motoyuki Shiga 2 , Nisanth N Nair 1
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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−1 accuracy, ensuring a safe usage for broad applications in computational chemistry.
中文翻译：
基于平均力的温度加速切片采样：高维自由能景观的有效重建
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，可在存在约束偏差的情况下获得的切片窗口中重新加权和拼接高维概率分布。WHAM 需要 TASS 窗口彼此靠近以实现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，这可以在没有 WHAM 后处理的情况下使用较少数量的窗口进行准确计算。该技术的应用证明了丙氨酸二肽和三肽在真空中计算其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强大的。景观在千卡摩尔内计算−1精度，确保在计算化学的广泛应用中安全使用。
更新日期：2021-09-09
中文翻译：
基于平均力的温度加速切片采样：高维自由能景观的有效重建
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，可在存在约束偏差的情况下获得的切片窗口中重新加权和拼接高维概率分布。WHAM 需要 TASS 窗口彼此靠近以实现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，这可以在没有 WHAM 后处理的情况下使用较少数量的窗口进行准确计算。该技术的应用证明了丙氨酸二肽和三肽在真空中计算其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强大的。景观在千卡摩尔内计算−1精度，确保在计算化学的广泛应用中安全使用。
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