xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states
xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states
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xTRAM：根据多个热力学状态下的时间相关模拟数据估计平衡期望
DOI：
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Frank No'e
中科院分区：
文献类型：
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作者：
A. Mey;Hao Wu;Frank No'e
计算复杂系统的平衡性质，如自由能差，经常受到动力学中罕见事件的阻碍。可以使用增强的采样方法，以便通过例如使用高温（如在并行回火中）或使用偏置电位（如在伞形采样的情况下）进行模拟来加速采样。感兴趣的热力学状态的平衡性质（例如，最低温度或无偏电势）可以使用诸如加权直方图分析方法或多状态班尼特接受比（MBAR）的重新加权估计器来计算。加权直方图分析方法和MBAR产生无偏估计，模拟样本来自它们各自的热力学状态下的全局平衡-对于某些模拟，例如明确溶剂化的生物分子的大的平行回火系综，这一要求可能非常昂贵。在这里，我们介绍的过渡为基础的重新加权分析方法（TRAM）-一类估计，利用马尔可夫模型的想法，只需要模拟数据在局部平衡的配置空间的子集内。我们制定的扩展TRAM（xTRAM）估计，证明是渐近无偏和MBAR的推广。使用四个示例性的系统不同的复杂性，我们证明了改进的收敛性（范围从两倍的改善到几个数量级）的xTRAM相比，直接计数估计和MBAR，相对于投资的模拟工作。最后，我们介绍了一个随机交换的模拟协议，可以与xTRAM一起使用，获得了数量级的优势，比需要从全局平衡采样的约束的模拟协议。
Computing the equilibrium properties of complex systems, such as free energy differences, is often hampered by rare events in the dynamics. Enhanced sampling methods may be used in order to speed up sampling by, for example, using high temperatures, as in parallel tempering, or simulating with a biasing potential such as in the case of umbrella sampling. The equilibrium properties of the thermodynamic state of interest (e.g., lowest temperature or unbiased potential) can be computed using reweighting estimators such as the weighted histogram analysis method or the multistate Bennett acceptance ratio (MBAR). weighted histogram analysis method and MBAR produce unbiased estimates, the simulation samples from the global equilibria at their respective thermodynamic state--a requirement that can be prohibitively expensive for some simulations such as a large parallel tempering ensemble of an explicitly solvated biomolecule. Here, we introduce the transition-based reweighting analysis method (TRAM)--a class of estimators that exploit ideas from Markov modeling and only require the simulation data to be in local equilibrium within subsets of the configuration space. We formulate the expanded TRAM (xTRAM) estimator that is shown to be asymptotically unbiased and a generalization of MBAR. Using four exemplary systems of varying complexity, we demonstrate the improved convergence (ranging from a twofold improvement to several orders of magnitude) of xTRAM in comparison to a direct counting estimator and MBAR, with respect to the invested simulation effort. Lastly, we introduce a random-swapping simulation protocol that can be used with xTRAM, gaining orders-of-magnitude advantages over simulation protocols that require the constraint of sampling from a global equilibrium.
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DOI：
10.1063/1.3592153
发表时间：
2011-06
期刊：
The Journal of chemical physics
影响因子：
--
作者：
Jan-Hendrik Prinz;J. Chodera;V. Pande;William Swope;Jeremy C. Smith;F. Noé
通讯作者：
Jan-Hendrik Prinz;J. Chodera;V. Pande;William Swope;Jeremy C. Smith;F. Noé
影响因子：
4.4
作者：
Shirts, Michael R.;Chodera, John D.
通讯作者：
Chodera, John D.
影响因子：
4.4
作者：
Prinz, Jan-Hendrik;Wu, Hao;Noe, Frank
通讯作者：
Noe, Frank
影响因子：
5.5
作者：
Eastman P;Friedrichs MS;Chodera JD;Radmer RJ;Bruns CM;Ku JP;Beauchamp KA;Lane TJ;Wang LP;Shukla D;Tye T;Houston M;Stich T;Klein C;Shirts MR;Pande VS
通讯作者：
Pande VS
影响因子：
3.3
作者：
Gallicchio, E;Andrec, M;Levy, RM
通讯作者：
Levy, RM