done, bug #402<br><br><div class="gmail_quote">On Tue, Mar 9, 2010 at 11:44 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 class="im">On 2010-03-09 20.01, Joe Joe wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I also just tried on a different ALA and got the same problem.<br>
</blockquote>
<br></div>
can you please submit a bugzilla and upload files to reproduce the problem?<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
Ilya<br>
<br>
<br>
On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe <<a href="mailto:ilchorny@gmail.com" target="_blank">ilchorny@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:ilchorny@gmail.com" target="_blank">ilchorny@gmail.com</a>>> wrote:<br>
<br>
I am looking the the gmxdump output and everything seems consistent.<br>
The only difference is that the numbering in the index file starts<br>
at 1 whereas in the gmxdump the arrays are indexed starting at 0.<br>
The coordinates look just fine.<br>
<br>
Thanks,<br>
<br>
Ilya<br>
<br>
<br>
<br>
On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe <<a href="mailto:ilchorny@gmail.com" target="_blank">ilchorny@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:ilchorny@gmail.com" target="_blank">ilchorny@gmail.com</a>>> wrote:<br>
<br>
I trjconv/ed xtc to pdb and loaded into vmd. The coordinates<br>
looked fine.<br>
<br>
I also<br>
<br>
tpbconv/ed topol.tpr to topol_subset.tpr.<br>
<br>
then I<br>
<br>
editconf/ed topol_subset.tpr to gro and looked at the<br>
coordinates. Index file matched and structure looked whole in vmd.<br>
<br>
I will try the gmxdump<br>
<br>
Thanks,<br>
<br>
Ilya<br>
<br>
<br>
<br>
<br>
On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel<br></div><div><div></div><div class="h5">
<<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 19.16, Joe Joe wrote:<br>
<br>
yep.<br>
<br>
Have you gmxdump/ed the xtc to check the coordinates are right?<br>
<br>
<br>
On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel<br>
<<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>><br>
<mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a><br>
<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<br>
trajectory using g_dist. I am<br>
trying to calculate the CA-CB distance of an<br>
Alanine residue but<br>
I get<br>
NAN in all the distance columns. It works for<br>
the other residues<br>
I've<br>
tried (i.e. SER, VAL). I am using vsites in my<br>
simulation and I<br>
think it<br>
may have some thing to do with the way gromacs<br>
outputs the CB<br>
positions<br>
in the xtc file when the CB is part of the vsite<br>
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>
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-- <br>
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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>
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