[gmx-users] PCA comparison

Berk Hess gmx3 at hotmail.com
Thu Oct 23 13:48:16 CEST 2008


The cosine content can only be use for "negative" conclusions.
If it is high, the sampling is bad.
If it is low, the sampling can be either good or bad, it doesn't tell.

The overlap is a much better measure.
Since it is so low, you have bad sampling.

Have you looked at the eigenvector inner products to check
if the pc directions change, or if only the eigenvalue change?


> Date: Thu, 23 Oct 2008 13:10:23 +0200
> From: rcsqtc at iiqab.csic.es
> To: gmx-users at gromacs.org
> Subject: [gmx-users] PCA comparison
> Dear all,
> We are performing some PCA analysis of several 22ns trajectories of a
> protein hexamer at different temperatures (280, 300, 320K). We expected
> to see a similar movement decribed by the ~10 lowest PCA's.
> their overlap is very poor: Below 0.35, and the diagonal elements are
> not remarkably higher than the rest. If we split one of the trajectories
> into to 11ns ones and do the same, again the overlap obtained is below
> 0.44 in all cases and there is no clear diagonal. 11ns is quite a long
> trajectory so I expected to see the same type of movement described by
> both 11ns fragments. Here are the cosine contents of the whole 22 ns
> trajectory and the two fragments. Except for the 1st pc, the rest seem
> well sampled: shouldn't they agree?
> 22ns:
> Cosine content  PC1 0.956255
> Cosine content  PC2 0.00428106
> Cosine content  PC3 0.000162083
> 1st 11ns:
> Cosine content  PC1 0.923261
> Cosine content  PC2  0.0217681
> Cosine content  PC3 0.0135543
> 2nd 11ns:
> Cosine content  PC1 0.786694
> Cosine content  PC2 0.1654
> Cosine content  PC3 0.000335589
> Are we doing something wrong? Is this the exptected behaviour?
> This is what we do to calculate the PCA's (10ns of equilibration removed):
> g_covar -f trajectory.xtc -b 10000 -e 21000 -s structure.pdb -o
> eigenval-T300-A.xvg -v eigenvec-T300-A.trr -av average-pca-T300-A.pdb
> g_covar -f trajectory.xtc -b 21020 -s structure.pdb -o
> eigenval-T300-B.xvg -v eigenvec-T300-B.trr -av average-pca-T300-B.pdb
> and to compare them:
> g_anaeig -inpr T300-A-B.xpm -v eigenvec-T300-A.trr -v2
> eigenvec-T300-B.trr -first 1 -last 10
> Thanks for your help and suggestions!
> Ramon
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