[gmx-users] g_dist and vsites

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 9 19:15:22 CET 2010

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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