[gmx-users] principal component analysis

pratibha kapoor kapoorpratibha7 at gmail.com
Fri Sep 27 14:03:17 CEST 2013

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 0.08Chain buried area0.74-0.30-0.41 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- chain B factor
0.090.75-0.050.64 -0.010.00- 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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