[gmx-users] Problems with Jacobi diagonalization

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 1 20:12:25 CEST 2009

Hi Dayle,

Errm, really, the only cases I know of this error to occur is when I
had a mismatch between the reference and trajectory. Did you specify
xtc-groups? Did you shuffle the system? How did you assert that you
have matching series? Have you tried using the reference and the
trajectory to convert (part of) the trajectory to .pdb and visualize?
If all else fails, can you send (a link to) an archive containing a
single frame from the trajectory and the reference?



2009/4/1 Dayle Smith <daylemariesmith at gmail.com>:
> Greetings---
> I'm working with a DNA system, and all of the routines I've worked with that
> require Jacobi diagonalization (g_covar, g_rms, etc) fail with the "Too many
> iterations in routine JACOBI" error. I'm using gromacs-3.3.3 with ffamber99
> on the NCSA Mercury cluster. I've searched the archives, and I've found
> several entries in which users are advised to check that the coordinates in
> the trajectory and structure files match (mine do). I've also tried running
> covariance analysis on a small ligand molecule, and I get the same error. I
> can get g_covar to work with -nofit, but then I can't run g_anaeig.
> I'm eagerly looking forward to your suggestions!
> Have a great day,
> Dayle Smith
> Department of Physics
> Whitman College
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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