[gmx-users] Overlap between PC motions

Miguel Ángel Mompeán García mig.mompean at gmail.com
Thu May 30 12:26:27 CEST 2013

Dear all,

I posted some days ago an issue regarding overlap values. If any of you is
experienced with this I would appreciate some comments. Please find below
the mentioned post:

I am doing PCA on a 110ns run.
When calculating the subspace overlap from independent PCA performed in
different time windows, I expect the overlap to be 1 only when the time
interval is equal to 110ns, since both covariance matrices are identical.
However, I found that from the interval 0-70 forwards (I'm increasing each
window in 10ns) the overlap reaches that value. Is this expected? From the
rmsd, cosine content and visual inspection of the trajectory I expected
small changes from this point till the total time, but not the two matrices
being equal... Am I doing something wrong or this may happen?

Here is my data set of results:

Normalized Shape DT
0.611        0.638    0-10ns
0.616        0.650    0-20ns
0.646        0.671    0-30ns
0.656        0.678    0-40ns
0.659        0.683    0-50ns
0.873        0.919    0-60ns
1.000        1.000    0-70ns
1.000        1.000    0-80ns
1.000        1.000    0-90ns
1.000        1.000    0-100ns
1.000        1.000    0-110ns = Ttot


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