Department of Physics, Keio University, Yokohama, Kanagawa 223-8522, Japan.
J Chem Phys. 2011 Oct 28;135(16):164102. doi: 10.1063/1.3652959.
This article reports the first attempt to apply the relaxation mode analysis method to a simulation of a biomolecular system. In biomolecular systems, the principal component analysis is a well-known method for analyzing the static properties of fluctuations of structures obtained by a simulation and classifying the structures into some groups. On the other hand, the relaxation mode analysis has been used to analyze the dynamic properties of homopolymer systems. In this article, a long Monte Carlo simulation of Met-enkephalin in gas phase has been performed. The results are analyzed by the principal component analysis and relaxation mode analysis methods. We compare the results of both methods and show the effectiveness of the relaxation mode analysis.
本文报道了首次尝试将弛豫模式分析方法应用于生物分子系统的模拟。在生物分子系统中，主成分分析是一种分析通过模拟获得的结构波动的静态特性并将结构分类为若干组的知名方法。另一方面，弛豫模式分析已被用于分析均聚物系统的动态特性。在本文中，对气相中的 Met-enkephalin 进行了长的蒙特卡罗模拟。通过主成分分析和弛豫模式分析方法对结果进行分析。我们比较了这两种方法的结果，并展示了弛豫模式分析的有效性。
