[gmx-users] my own routine

[Isabella Daidone]

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 
Isabella


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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