Hello,
Thank you for your reply. I used .tpr file genarated from grompp for
mdrun which generated the .trr file.
I have not specified xtc-grps.
Regards,
Nishtha
On Sat, Jan 24, 2009 at 11:02 PM, Tsjerk Wassenaar <tsje...@gmail.com>wrote:
> Hi,
>
> On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey <nisht...@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
>
> --
> 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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