[gmx-users] g_dist and vsites

[David van der Spoel]

On 2010-03-09 20.01, Joe Joe wrote:
> I also just tried on a different ALA and got the same problem.

can you please submit a bugzilla and upload files to reproduce the problem?

>
> Ilya
>
>
> On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe <ilchorny at gmail.com
> <mailto:ilchorny at gmail.com>> wrote:
>
>     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.
>
>     Thanks,
>
>     Ilya
>
>
>
>     On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe <ilchorny at gmail.com
>     <mailto:ilchorny at gmail.com>> wrote:
>
>         I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates
>         looked fine.
>
>         I also
>
>         tpbconv/ed topol.tpr to topol_subset.tpr.
>
>         then I
>
>         editconf/ed topol_subset.tpr to gro and looked at the
>         coordinates. Index file matched and structure looked whole in vmd.
>
>         I will try the gmxdump
>
>         Thanks,
>
>         Ilya
>
>
>
>
>         On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
>         <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>             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>
>                 <mailto: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>
>                 <mailto: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 <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