Bonomi M, Barducci A, Parrinello M
Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, via Buffi 13, CH-6900 Lugano, Switzerland.
J Comput Chem. 2009 Aug;30(11):1615-21. doi: 10.1002/jcc.21305.
Metadynamics is a widely used and successful method for reconstructing the free-energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well-tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation.
元动力学是一种广泛使用且成功的方法，用于根据少量适当选择的集体变量重构复杂系统的自由能表面。这是通过对系统动力学施加偏置来实现的。作用于集体变量的偏置会扭曲其他变量的概率分布。在此，我们提出一种简单的重加权算法，用于从温和元动力学模拟中恢复任何变量的无偏概率分布。我们通过从二维甚至一维元动力学模拟中重构丙氨酸二肽四个主链二面角的分布，展示了重加权过程的效率。
