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
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.
If you specify xtc-grps, that is what is saved in the simulation; it has no
effect on the coordinates processed by grompp. If you are using a .pdb or .gro
file as input into grompp that has both SOL and TDR, then you will *always* have
those atoms in the .tpr file. Changes to the .mdp file have no impact
whatsoever on the coordinate contents of the .tpr file.
There are two potential solutions, and the only way to solve your issue will be
to do one of the following:
1. Use tpbconv to create a new .tpr file with only TDR (select TDR as the output
group when prompted)
2. Strip your coordinate file of water and re-process with grompp, such that
grompp is only interpreting the coordinates of TDR
Option #1 is simpler; option #2 is instructive in terms of understanding how the
.tpr file is assembled and how coordinates are interpreted.
-Justin
~Dayle
On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
<tsje...@gmail.com <mailto:tsje...@gmail.com>
<mailto:tsje...@gmail.com <mailto: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
<mailto:daylemariesm...@gmail.com>
<mailto:daylemariesm...@gmail.com
<mailto: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
>
--
========================================
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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