[gmx-users] my own routine

Berk Hess gmx3 at hotmail.com
Tue Apr 20 13:38:00 CEST 2004

>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
>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?


Play online games with your friends with MSN Messenger 

More information about the gromacs.org_gmx-users mailing list