[gmx-users] Problems with Jacobi diagonalization

[TJ Piggot]

Or rather than modifying the .top use tpbconv with an index file to 
generate a new .tpr

Tom

--On Wednesday, April 01, 2009 21:15:34 -0400 "Justin A. Lemkul" 
<jalemkul at vt.edu> wrote:

>
>
> 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
>>             >
>>
>>
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php



----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.