Vanden-Eijnden Eric
Courant Institute, New York University, 251 Mercer Street, New York 10012, USA.
J Comput Chem. 2009 Aug;30(11):1737-47. doi: 10.1002/jcc.21332.
A few recent techniques to calculate free energies in the context of molecular dynamics simulations are discussed: temperature-accelerated molecular dynamics, which is a method to explore fast the important regions in the free energy landscape associated with a set of continuous collective variables without having to know where these regions are beforehand; the single sweep method, which is a variational method to interpolate the free energy globally given a set of mean forces (i.e., a set of gradients of the free energy) calculated at specific points, or centers, on the free energy landscape; and a Voronoi-based free energy method for the calculation of the free energy of the Voronoi tessellation associated with a set of centers. We also discuss how this last technique can be used in conjunction with the string method, and how kinetic information such as reaction rates can be calculated by milestoning using the edges of a Voronoi tessellation as milestones.
温度加速分子动力学，这是一种无需事先知道这些区域位置就能快速探索与一组连续集体变量相关的自由能景观中重要区域的方法；单扫描方法，这是一种变分方法，可在给定一组在自由能景观特定点或中心计算的平均力（即自由能的一组梯度）的情况下全局插值自由能；以及一种基于Voronoi的自由能方法，用于计算与一组中心相关的Voronoi镶嵌的自由能。我们还讨论了最后一种技术如何与弦方法结合使用，以及如何通过将Voronoi镶嵌的边用作里程碑进行里程碑分析来计算诸如反应速率等动力学信息。
