Hello,<br> Thank you for your reply. I used .tpr file genarated from grompp for mdrun which generated the .trr file.<br>I have not specified xtc-grps.<br>Regards,<br>Nishtha<br><br><div class="gmail_quote">On Sat, Jan 24, 2009 at 11:02 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>
<div class="Ih2E3d"><br>
On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey <<a href="mailto:nishthap@gmail.com">nishthap@gmail.com</a>> wrote:<br>
> Hello everyone,<br>
> While trying to do the RMSD analysis of my trajectory<br>
> file I am facing the error " Too many iterations in routine JACOBI". I have<br>
> gone through the archives which suggests that such problem arises if there<br>
> is mismatch between the reference structure and trajectory. However in my<br>
> case the problem lies somewhere else because, using the same .tpr file and<br>
> .trr file I have done RMSD analysis earlier also and it worked fine.<br>
<br>
</div>The .tpr and the .trr files will correspond per definition, provided<br>
the former is used to generate the latter. This is not the case for<br>
the .xtc. My guess is you do have a mismatch. Did you specify<br>
xtc-grps? In that case you might want to extract a corresponding<br>
reference structure from your .tpr.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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