Hi Tsjerk,<br>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. <br>
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:<br><br>WARNING: number of atoms in tpx (29) and trajectory (29) do not match<br>
-------------------------------------------------------<br>Program g_covar, VERSION 3.3.3<br>Source code file: nrjac.c, line: 129<br>Fatal error:<br>Error: Too many iterations in routine JACOBI<br><br>So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?!<br>
<br>Thanks a lot,<br>Dayle<br><br><br><br><br><div class="gmail_quote">On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Dayle,<br>
<br>
Errm, really, the only cases I know of this error to occur is when I<br>
had a mismatch between the reference and trajectory. Did you specify<br>
xtc-groups? Did you shuffle the system? How did you assert that you<br>
have matching series? Have you tried using the reference and the<br>
trajectory to convert (part of) the trajectory to .pdb and visualize?<br>
If all else fails, can you send (a link to) an archive containing a<br>
single frame from the trajectory and the reference?<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
2009/4/1 Dayle Smith <<a href="mailto:daylemariesmith@gmail.com">daylemariesmith@gmail.com</a>>:<br>
<div><div></div><div class="h5">> Greetings---<br>
> I'm working with a DNA system, and all of the routines I've worked with that<br>
> require Jacobi diagonalization (g_covar, g_rms, etc) fail with the "Too many<br>
> iterations in routine JACOBI" error. I'm using gromacs-3.3.3 with ffamber99<br>
> on the NCSA Mercury cluster. I've searched the archives, and I've found<br>
> several entries in which users are advised to check that the coordinates in<br>
> the trajectory and structure files match (mine do). I've also tried running<br>
> covariance analysis on a small ligand molecule, and I get the same error. I<br>
> can get g_covar to work with -nofit, but then I can't run g_anaeig.<br>
><br>
> I'm eagerly looking forward to your suggestions!<br>
><br>
> Have a great day,<br>
> Dayle Smith<br>
> Department of Physics<br>
> Whitman College<br>
><br>
><br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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