[gmx-users] my own routine

Isabella Daidone i.daidone at caspur.it
Tue Apr 20 13:59:00 CEST 2004

I'm  calculating geometrical axes at every frame using ql77 for the
diagonalization. The problem is not the diagonalization.
The problem is the .xtc file because everything is OK when I check the
program on .gro formats while I get problems using the .xtc
trajectory. In fact everything is OK except for a couple of frames where
the simulation has been restarted
to continue after interruption. At these two frames I obtain wrong
results for the eigenvectors, for example the modulus is different from
the unity.
Is there a function to overcome the problem of these interrupted frames
using a .xtc trajectory?
thank you 

On Tue, 20 Apr 2004, Berk Hess wrote:

> >Hi,
> >I have adapted GROMACS template.c to calculate the eigenvectors of a
> >positional covariance matrix in time, i.e. frame per frame.
> >The program seems to work, except for a couple of frames, that
> >correspond to the points where the trajectory has been restarted after
> >interruption.
> >At these two frames the modulus of each eigenvector is completely
> >different from the
> >unity, while it should be one.
> >But when I check with the same program the single frames in format .gro,
> >I get the correct results.
> >Any suggestions?
> I don't understand what you want to do.
> For covariance something needs to vary.
> One frame is just static, so the covariance matrix is zero.
> Or do you mean you calculate the covariance matrix
> for frame 0, frame 0+1, frame 0+1+2 etc.?
> I have no idea what the program does, but the modulus of
> an eigenvector is one by definition, so this would indicate
> you made a programming error which has nothing to do
> with Gromacs itself.
> Or do you use the Gromacs diagonalization routine?
> Berk.
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