Thanks, Mark-<br>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!), <br>
<br>g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx<br><br>and I still get the Jacobi error:<br><br>Choose a group for the least squares fit<br>Group 0 ( TDR) has 29 elements<br>There is one group in the index<br>
<br>Choose a group for the covariance analysis<br>Group 0 ( TDR) has 29 elements<br>There is one group in the index<br>Calculating the average structure ...<br>Reading frame 0 time 0.000<br>-------------------------------------------------------<br>
Program g_covar, VERSION 3.3.3<br>Source code file: nrjac.c, line: 129<br><br>Fatal error:<br>Error: Too many iterations in routine JACOBI<br><br>~Dayle<br><br><br><div class="gmail_quote">On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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;"><div class="im">Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Dayle Smith wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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 <br>
</blockquote>
<br>
Indeed, that's the problem, then!<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
</blockquote>
<br>
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.<br>
</blockquote>
<br></div>
Or use tpbconv - this is the "other" application for that utility.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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