title: Relaxation mode analysis of a peptide system: comparison with principal component analysis.
abstract: 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.
authors: Department of Physics, Keio University, Yokohama, Kanagawa 223-8522, Japan. ayori@mail.rk.phys.keio.ac.jp
authors: Ayori
authors: A
authors: Mitsutake
authors: Hiromitsu
authors: H
authors: Iijima
authors: Hiroshi
authors: H
authors: Takano
mesh_terms: D003198:Computer Simulation; D004744:Enkephalin, Methionine / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D025341:Principal Component Analysis
chemical_list: D004744:Enkephalin, Methionine