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.
| Original language | English |
|---|---|
| Article number | 164102 |
| Journal | Journal of Chemical Physics |
| Volume | 135 |
| Issue number | 16 |
| DOIs | |
| Publication status | Published - 2011 Oct 28 |
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ASJC Scopus subject areas
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry
- Medicine(all)
Cite this
Relaxation mode analysis of a peptide system : Comparison with principal component analysis. / Mitsutake, Ayori; Iijima, Hiromitsu; Takano, Hiroshi.
In: Journal of Chemical Physics, Vol. 135, No. 16, 164102, 28.10.2011.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Relaxation mode analysis of a peptide system
T2 - Comparison with principal component analysis
AU - Mitsutake, Ayori
AU - Iijima, Hiromitsu
AU - Takano, Hiroshi
PY - 2011/10/28
Y1 - 2011/10/28
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=80555139848&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=80555139848&partnerID=8YFLogxK
U2 - 10.1063/1.3652959
DO - 10.1063/1.3652959
M3 - Article
C2 - 22047223
AN - SCOPUS:80555139848
VL - 135
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 16
M1 - 164102
ER -