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 <tsje...@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 <daylemariesm...@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 > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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