[gmx-users] principal component analysis

[Tsjerk Wassenaar]

Hi Prathiba,

I think you should have a look at the "Functional Mode Analysis" method
from Bert de Groot's lab.

Cheers,

Tsjerk


On Sat, Sep 28, 2013 at 8:13 AM, pratibha kapoor
<kapoorpratibha7 at gmail.com>wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.