[gmx-users] Overlap between PC motions

[Miguel Ángel Mompeán García]

Hi Tsjerk,

Thanks for the reply! So, let me see if I am getting the things right. The
same fitting structure is used for the overlap calculation. Since the
averaged structure is used for the covariance matrices, this is the reason
why the relaxation is included. Am I right?
The overall behavior of the system is that the structure keeps very
"compact" and one additional hydrogen bond between two residues is formed
at ~60ns, and stable till the end of the run, as computed with g_hbond.
That interaction is already present in the average structure. So if I
understood properly your comment, from the time window 0-70 up to the end,
 there will not be significant contributions to the covariance matrix.

Thanks for your valuable comments. Highly appreciated!


2013/5/30 Tsjerk Wassenaar <tsjerkw at gmail.com>

> 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,
>
> Tsjerk
>
>
>
> 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
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>