[gmx-users] g_rms: Too many iterations in routine JACOBI

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jan 24 18:32:20 CET 2009


On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey <nishthap at gmail.com> wrote:
> Hello everyone,
>                      While trying to do the RMSD analysis of my trajectory
> file I am facing the error " Too many iterations in routine JACOBI". I have
> gone through the archives which suggests that such problem arises if there
> is mismatch between the reference structure and trajectory. However in my
> case the problem lies somewhere else because, using the same .tpr file and
> .trr file I have done RMSD analysis earlier also and it worked fine.

The .tpr and the .trr files will correspond per definition, provided
the former is used to generate the latter. This is not the case for
the .xtc. My guess is you do have a mismatch. Did you specify
xtc-grps? In that case you might want to extract a corresponding
reference structure from your .tpr.

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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