[gmx-users] g_dist and vsites

[David van der Spoel]

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
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> 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.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se