[gmx-users] Problems with Jacobi diagonalization

[Justin A. Lemkul]

Dayle Smith wrote:
> 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?!

I think the output error message is bizarre, but you still have a number of 
atoms in the .tpr that does not match the .xtc.  If your simulation is of TDR 
and SOL, then those groups will be in your topol.tpr.  If your xtc-grps specify 
only TDR, then there will be a coordinate mismatch.  Run the following:

gmxcheck -c topol.tpr
gmxcheck -f traj.xtc

and see if gmxcheck reports the same number of atoms in both files.  This is the 
quickest way to know for sure.

-Justin

> 
> Thanks a lot,
> Dayle
> 
> 
> 
> 
> On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar <tsjerkw at gmail.com 
> <mailto: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
>     <mailto: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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> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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