[gmx-users] Overlap between PC motions

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 30 12:34:28 CEST 2013

Hi Miguel,

Sorry for not responding earlier, but the question isn't really simple :)
What you do is determining the covariance matrix from the start up to a
certain point and see for different end points what the overlap is with the
covariance matrix from the whole. This means that in all cases, the
relaxation of the system is included, and this is the dominant contribution
to your covariance matrix. At some point, the system has reached the region
around B and then stays there. All kinds of things may be happening, but
they're overwhelmed by the changes associated with the relaxation. Hence,
the part of the trajectory after 70 ns doesn't contribute significantly to
the covariance matrix anymore.

Hope it helps,


On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García <
mig.mompean at gmail.com> wrote:

> 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
> Regards,
> Miguel
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Tsjerk A. Wassenaar, Ph.D.

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