[gmx-users] Trajectory analysis

Oleg Katchanov oleg at drug.org.ru
Wed Feb 20 12:03:19 CET 2002

Hi to all!

I'm a new user of GROMACS 3.0, therefore my question may be  the result
of insufficient understanding. In case of this, sorry in advance.:)
Advise me, please, which metod of analysis of the trajectory is
preferable for me, if I want to get the information about the
slow-freequency motion in the peptide molecule? How I understand, it
must be the normal mode analysis - the art of harmonic analysis, or the
covariance analysis of the trajectory matrix. But I have a problem.
I want to analyze the trajectory of the peptide-molecule with a
covariance analysis:

g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -av

where the topol.tpr is the same used by mdrun for calculating the
And when I want to see the eigenvectors trajectory file:

ngmx -f eigenvec.trr -s topol.tpr

I see allways: "Fatal error: Error: Zero Length Vector - No View
Specified "
In the case of NM analysis the result is the same.:(
What I'm doing wrong? I read the manual attentively, but I still don't

Thank you in advance,
Katchanov Oleg.

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