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 <[email protected]
<mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]>>:
> 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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--
========================================
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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