yep.<br><br><div class="gmail_quote">On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5">On 2010-03-09 19.09, Joe Joe wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi I am trying to post process and xtc trajectory using g_dist. I am<br>
trying to calculate the CA-CB distance of an Alanine residue but I get<br>
NAN in all the distance columns. It works for the other residues I've<br>
tried (i.e. SER, VAL). I am using vsites in my simulation and I think it<br>
may have some thing to do with the way gromacs outputs the CB positions<br>
in the xtc file when the CB is part of the vsite network. Any thoughs?<br>
<br>
Thanks,<br>
<br>
Ilya<br>
<br>
</blockquote></div></div>
Are you sure your index file matches the xtc/tpr?<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br><font color="#888888">
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