I am looking the the gmxdump output and everything seems consistent. The only difference is that the numbering in the index file starts at 1 whereas in the gmxdump the arrays are indexed starting at 0. The coordinates look just fine.<div>
<br></div><div>Thanks,</div><div><br></div><div>Ilya</div><div><br><div><br></div><div><br><div class="gmail_quote">On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe <span dir="ltr"><<a href="mailto:ilchorny@gmail.com">ilchorny@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">I trjconv/ed xtc to pdb and loaded into vmd. The coordinates looked fine. <div><br></div><div>I also </div><div><br></div>
<div>tpbconv/ed topol.tpr to topol_subset.tpr.</div><div><br></div><div>then I </div><div><br></div>
<div>editconf/ed topol_subset.tpr to gro and looked at the coordinates. Index file matched and structure looked whole in vmd. </div><div><br></div><div>I will try the gmxdump</div><div><br></div><div>Thanks,</div><div><br>
</div><div>Ilya</div><div><div></div><div class="h5"><div><br></div><div><br></div><div><br><br><div class="gmail_quote">On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">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">On 2010-03-09 19.16, Joe Joe wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
yep.<br>
</blockquote>
Have you gmxdump/ed the xtc to check the coordinates are right?<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
<br>
On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel<br></div><div>
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br>
On 2010-03-09 19.09, Joe Joe wrote:<br>
<br>
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<br>
I get<br>
NAN in all the distance columns. It works for the other residues<br>
I've<br>
tried (i.e. SER, VAL). I am using vsites in my simulation and I<br>
think it<br>
may have some thing to do with the way gromacs outputs the CB<br>
positions<br>
in the xtc file when the CB is part of the vsite network. Any<br>
thoughs?<br>
<br>
Thanks,<br>
<br>
Ilya<br>
<br>
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></div>
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