Abstract
A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.
| Original language | English |
|---|---|
| Article number | 023803 |
| Journal | Journal of the Physical Society of Japan |
| Volume | 82 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - 2013 Feb |
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Keywords
- Molecular dynamics
- Principal component analysis
- Protein
- Relaxation mode analysis
- Simulation
ASJC Scopus subject areas
- Physics and Astronomy(all)
Cite this
Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of human lysozyme. / Nagai, Toshiki; Mitsutake, Ayori; Takano, Hiroshi.
In: Journal of the Physical Society of Japan, Vol. 82, No. 2, 023803, 02.2013.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of human lysozyme
AU - Nagai, Toshiki
AU - Mitsutake, Ayori
AU - Takano, Hiroshi
PY - 2013/2
Y1 - 2013/2
N2 - A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.
AB - A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.
KW - Molecular dynamics
KW - Principal component analysis
KW - Protein
KW - Relaxation mode analysis
KW - Simulation
UR - http://www.scopus.com/inward/record.url?scp=84874169983&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84874169983&partnerID=8YFLogxK
U2 - 10.7566/JPSJ.82.023803
DO - 10.7566/JPSJ.82.023803
M3 - Article
VL - 82
JO - Journal of the Physical Society of Japan
JF - Journal of the Physical Society of Japan
SN - 0031-9015
IS - 2
M1 - 023803
ER -