BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification†,Physical Chemistry Chemical Physics

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BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification†
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2018-01-04 00:00:00 , DOI: 10.1039/c7cp07573a
Xiaohui Wang _{1,

2,

3,

4,

5} , Xingzhao Tu _{6,

7,

8} , John Z. H. Zhang _{1,

2,

3,

4,

5} , Zhaoxi Sun _{1,

2,

3,

4,

5}

Affiliation

Following the previously proposed equilibrate-state sampling based adaptive sampling regime Optimum Bennett Acceptance Ratio (OBAR), we introduce its nonequilibrium extension, the Optimum Crooks’ Equation (OCE) in the current work. The efficiency of the NonEquilibrium Work (NEW) stratification is improved by adaptively manipulating the significance of each nonequilibrium realization followed by importance sampling. As is exhibited in the equilibrium case, the nonequilibrium extension outperforms the simple equal time rule used in nonequilibrium stratification in the sense of minimizing the total variance of the free energy estimate. The speedup of this non-equal time rule is more than 1-fold. The Time Derivative of total Variance (TDV) proposed for the OBAR criterion is extended to determine the importance of each nonequilibrium transformation, which is linearly dependent on the variance. The TDV in the nonequilibrium case gives a totally different importance rank from the standard errors of the free energy differences and OBAR TDV due to the duration of nonequilibrium pulling being added into the OCE equation. The performance of the OCE workflow is demonstrated in the solvation of several small molecules with a series of lambda increments and relaxation times between successive perturbations. To the best of our knowledge, such a nonequilibrium adaptive sampling regime in alchemical transformation is unprecedented.

中文翻译：

基于BAR的最佳自适应采样方案，用于炼金术转化中的方差最小化：非平衡分层†

继先前提出的基于平衡状态采样的自适应采样机制最佳Bennett接受率（OBAR）之后，我们在当前工作中介绍了其非平衡扩展，即最佳Crooks方程（OCE）。通过对每个非平衡实现的重要性进行适应性操作，然后进行重要性抽样，可以提高非平衡工作（NEW）分层的效率。正如在平衡情况下显示的那样，从最小化自由能估计值的总方差的角度来看，非平衡扩展优于非平衡分层中使用的简单等时规则。此非相等时间规则的加速超过1倍。为OBAR标准建议的总方差时间导数（TDV）已扩展，以确定每个非平衡变换的重要性，它线性地取决于方差。由于将非平衡拉拔的持续时间添加到OCE方程中，因此非平衡情况下的TDV与自由能差和OBAR TDV的标准误差的重要性等级完全不同。OCE工作流程的性能在几个小分子的溶剂化过程中得到证明，这些小分子在一系列连续扰动之间具有一系列的λ增量和弛豫时间。据我们所知，在炼金术转化中这种非平衡自适应采样机制是前所未有的。OCE工作流程的性能在几个小分子的溶剂化过程中得到证明，这些小分子在一系列连续扰动之间具有一系列的λ增量和弛豫时间。据我们所知，在炼金术转化中这种非平衡自适应采样机制是前所未有的。OCE工作流程的性能在几个小分子的溶剂化过程中得到证明，这些小分子在一系列连续扰动之间具有一系列的λ增量和弛豫时间。据我们所知，在炼金术转化中这种非平衡自适应采样机制是前所未有的。

更新日期：2018-01-04

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