[gmx-users] Problems with Jacobi diagonalization

[Justin A. Lemkul]

Dayle Smith wrote:
> 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 

Indeed, that's the problem, then!

> 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.

You haven't really changed anything.  The xtc-grps parameter defines what was 
saved in the simulation.  Setting it after the fact does not affect the 
already-produced .xtc file.  What you need is a .tpr file that contains only 
TDR, so you would have to make modifications to your .top in order to generate 
this TDR-only .tpr file.

-Justin

> ~Dayle
> 
> On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 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>
>         <mailto: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>
>            <mailto: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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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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