On 2010-03-09 19.16, Joe Joe wrote:
yep.
Have you gmxdump/ed the xtc to check the coordinates are right?
On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
<[email protected] <mailto:[email protected]>> wrote:
On 2010-03-09 19.09, Joe Joe wrote:
Hi I am trying to post process and xtc trajectory using g_dist. I am
trying to calculate the CA-CB distance of an Alanine residue but
I get
NAN in all the distance columns. It works for the other residues
I've
tried (i.e. SER, VAL). I am using vsites in my simulation and I
think it
may have some thing to do with the way gromacs outputs the CB
positions
in the xtc file when the CB is part of the vsite network. Any
thoughs?
Thanks,
Ilya
Are you sure your index file matches the xtc/tpr?
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] <mailto:[email protected]>
http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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