[gmx-users] principal component analysis

[Tsjerk Wassenaar]

Hi Pratibha,

The table is all garbled, and your description insufficiently clear for us
to form a mental picture of what you want, what you've tried to get that,
where it goes wrong, or where you get stuck, and how we can help you on the
right track again.

Cheers,

Tsjerk


On Fri, Sep 27, 2013 at 2:03 PM, pratibha kapoor
<kapoorpratibha7 at gmail.com>wrote:

> Dear all gmx users
>
> I would like to calculate pc loadings for various integrated factors in the
> form of following sample table:
> Integrated factorsPC1PC2PC3 PC4PC5PC6PC7PC8 PC9PC10Total nonpolar surface
> area0.60 -0.07-0.76-0.11-0.060.11 0.05-0.160.06-0.02Chain exposed area 0.92
> -0.14-0.050.12 0.230.200.09-0.07-0.03 0.08Chain buried area0.74-0.30-0.41
> 0.120.240.260.05 0.03-0.060.21Chain unpolar exposed area 0.71-0.08-0.630.02
> 0.03 0.280.00-0.060.08-0.03 Chain unpolar buried area0.69-0.23-0.580.06
> 0.12
> 0.17-0.100.20-0.16 -0.01Main chain B factor0.120.77-0.06
> 0.62-0.01-0.01-0.080.01
> 0.050.04Side chain B factor0.07 0.74-0.050.66-0.01
> 0.01-0.030.000.100.01Whole chain B factor
> 0.090.75-0.050.64 -0.010.00-0.050.010.08 0.02Average number of
> cavities-0.02
> -0.43 0.72-0.090.340.10-0.19 0.170.310.09Average volume of cavity -0.040.14
> 0.63-0.47-0.48 0.350.020.11-0.010.06 Content of Helix 0.870.090.00-0.41
> 0.17
> -0.10-0.09-0.12 0.130.00and so on..
> Please suggest me the way to proceed.
> I have done cartesian principal component analysis using
> g_covar -f *.xtc -s *.tpr
> and using g_anaeig
> This way I could get principal components. But then how to dissect each pc
> in terms of above integrated factors?
> Any help is appreciated.
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-- 
Tsjerk A. Wassenaar, Ph.D.