[gmx-users] Problems with Jacobi diagonalization
daylemariesmith at gmail.com
Thu Apr 2 03:12:31 CEST 2009
Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in
file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is the SOL
atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck
shows that the number of atoms in topol.tpr is 12284, but I still can't get
g_covar to work. Maybe these are unrelated problems, I'm not sure.
On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> 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.
>> Thanks a lot,
>> 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?
>> 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
>> > on the NCSA Mercury cluster. I've searched the archives, and I've
>> > 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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