Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, Via Celoria 16, I-20133 Milano, Italy.
Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy.
J Chem Phys. 2018 May 14;148(18):184114. doi: 10.1063/1.5030339.
Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimental data, and it has been shown that replica-averaged simulations, restrained using a static potential, are a practical and powerful implementation of such a principle. Here we show that replica-averaged simulations restrained using a time-dependent potential are equivalent to the principle of maximum caliber, the dynamic version of the principle of maximum entropy, and thus may allow us to integrate time-resolved data in molecular dynamics simulations. We provide an analytical proof of the equivalence as well as a computational validation making use of simple models and synthetic data. Some limitations and possible solutions are also discussed.
推理方法可用于整合实验信息和分子模拟。最大熵原理为使用平衡实验数据提供了一个框架,并且已经表明,使用静态势约束的复制平均模拟是该原理的一种实际且强大的实现。在这里,我们表明,使用时变势约束的复制平均模拟等同于最大口径原理,即最大熵原理的动态版本,因此,它可能使我们能够在分子动力学模拟中整合时间分辨数据。我们提供了等价性的分析证明以及使用简单模型和合成数据进行的计算验证。还讨论了一些限制和可能的解决方案。