Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-2325, USA.
Department of Chemistry, University of Chicago, Chicago, Illinois 60637-1454, USA.
J Chem Phys. 2018 Aug 21;149(7):072315. doi: 10.1063/1.5027494.
Expanded ensemble simulation is a powerful technique for enhancing sampling over a range of thermodynamic parameters. However, although the premise is relatively simple, running successful simulations in practice still presents something of an challenge. Three main difficulties exist: (1) the selection of the thermodynamic states, (2) the selection of the sampling weights, and (3) efficient sampling of the expanded parameter space. Here we consider these problems in the context of a pairwise linear response approach to the work fluctuation theorem. The approach offers comprehensive tactics for addressing the three difficulties and can be used as either an alternative or a complement to replica exchange simulations. Importantly, the results are trivially implemented for multi-dimensional parameter spaces and they recover results from the literature aimed at the special cases of simulated/parallel tempering and replica exchange umbrella sampling. Illustrative examples are shown using the NAMD simulation engine.
扩展集合模拟是一种强大的技术，可以增强在一系列热力学参数上的采样。然而，尽管前提相对简单，但在实践中运行成功的模拟仍然存在一定的挑战。主要存在三个困难：（1）热力学状态的选择，（2）采样权重的选择，以及（3）扩展参数空间的有效采样。在这里，我们考虑了在工作涨落定理的成对线性响应方法的背景下这些问题。该方法为解决三个困难提供了全面的策略，可以作为 replica 交换模拟的替代或补充。重要的是，结果对于多维参数空间是微不足道的实现，并且它们恢复了针对模拟/并行温度和 replica 交换伞状采样的特殊情况的文献中的结果。使用 NAMD 模拟引擎显示了说明性示例。
