[gmx-users] principal component analysis
pratibha kapoor
kapoorpratibha7 at gmail.com
Sat Sep 28 08:13:00 CEST 2013
Dear all users
I would like to calculate pc loadings for various integrated factors in the
form of following sample table:
Integrated Factors
PC1
PC2
PC3
PC4
PC5
PC6
PC7
PC8
PC9
PC10
Total non polar surface area
0.60
-0.07
-0.76
-0.11
0.08
0.05
-0.16
0.08
-0.01
0.02
Native contacts
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Content of helix
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Average volume of cavity
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Content of turns
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
Some value
I have done cartesian coordinate pca using g_covar and g_anaeig (using -s
and -f flags) in which I have supplied my reference structure file (which
contains atomic coordinates of structure after equilibration). This way I
could get eigenvalues, eigenvectors and principal components.
Now I would like to ask how can I disect these principal components in
terms of various properties such as those enlisted above.
Any help is appreciated.
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