[gmx-users] Problems with Jacobi diagonalization

Dayle Smith daylemariesmith at gmail.com
Thu Apr 2 03:58:09 CEST 2009

Thanks, Mark-
I re-ran a short MD simulation with TDR as the only xtc group, and used
tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar
with an index.ndx that contains only TPR (just to be safe!),

g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx

and I still get the Jacobi error:

Choose a group for the least squares fit
Group     0 (         TDR) has    29 elements
There is one group in the index

Choose a group for the covariance analysis
Group     0 (         TDR) has    29 elements
There is one group in the index
Calculating the average structure ...
Reading frame       0 time    0.000
Program g_covar, VERSION 3.3.3
Source code file: nrjac.c, line: 129

Fatal error:
Error: Too many iterations in routine JACOBI


On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Justin A. Lemkul 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.
> Or use tpbconv - this is the "other" application for that utility.
> Mark
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