[gmx-users] Problems with Jacobi diagonalization

[Dayle Smith]

Hi Tsjerk,
Thank you for your quick and helpful response. I defined "xtc_grps  = TDR"
in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top
-o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with
-np 8.
I'm afraid that I don't understand what "shuffling" or "matching series"
refers to (a clue that I'm doing something wrong).  This g_covar error
message is probably another clue:

WARNING: number of atoms in tpx (29) and trajectory (29) do not match
-------------------------------------------------------
Program g_covar, VERSION 3.3.3
Source code file: nrjac.c, line: 129
Fatal error:
Error: Too many iterations in routine JACOBI

So the # of atoms is the same, but some other key ingredient doesn't match.
Can you please enlighten me?!

Thanks a lot,
Dayle




On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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?
>
> Cheers,
>
> Tsjerk
>
> 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
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