Hi Jason,
This is the explanation that came to my mind just before going to bed :D I
think you are right.
Thanks for the reply!
-Jose
On Tue, Jun 29, 2010 at 11:37 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> Why do you expect identical eigenvectors? I'd agree that the eigenvalues
> should all be nearly identical (though the RMS fit may be different based
> on
> the frame you fit to). However, wouldn't the cartesian representation of
> the eigenvectors depend on the orientation of the reference frame? I can
> imagine you'd get better agreement if you could find out how to rotate the
> first frame to fit the last frame, then apply those transformations to the
> one of the sets of eigenvectors.
>
> For the metric you're using: suppose in the extreme case that the last
> frame has undergone a 90 degree rotation in the X-Y plane (and Z has stayed
> the same). Then the same mode will be perpendicular in the two matrices
> you
> construct using each frame as a reference, and their similarity will
> *appear* to be 0 according to your criteria (I think it's basically just an
> inner product). However, they're really identical since they describe
> exactly the same motion.
>
> You or others may correct me here if I'm missing something obvious.
>
> Good luck!
> Jason
>
> On Tue, Jun 29, 2010 at 10:34 PM, Jose Borreguero <borreguero.gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > In ptraj, using *matrix mwcovar* produces very different set of modes if
> > one
> > uses different reference conformations to remove translations and
> > rotations.
> > Does anyone know why is this the case? I had assume that being the same
> > trajectory, the modes would be very similar. If the modes are to be a
> > property of the protein, they should be quite independent of the
> reference
> > conformation.
> >
> > This is the ptraj input file. Here I used the first conformation as
> > reference:
> > *trajin mdcrd
> > reference first.rst
> > rms reference :.CA
> > matrix mwcovar name pca :.CA out evecs_first.dat
> > *
> > I also have another input file using the last conformation as reference
> (*
> > last.rst* produces *evecs_last.dat*)
> >
> > As it turns out, modes in *evecs_first.dat *and *evecs_last.dat *are very
> > different! I compare the modes using the Hess metric:
> > *similarity = 1/N * Sum_i Sum_j (v_i w_j)^2,*
> > where *v_i* are the first *N* modes from *evecs_first.dat *and *w_j* are
> > the
> > first *N *modes from *evecs_last.dat*. There is a dot product between the
> > modes.
> >
> > Has anybody encountered such situation?
> >
> > Best regards,
> > -Jose M. Borreguero
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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>
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Received on Wed Jun 30 2010 - 06:00:19 PDT
