[gmx-users] Vizualization with VMD: no image appears

[rama david]

Dear,
   -o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file.
And then load it in vmd or pymol u can see it

On Wed, Nov 21, 2012 at 10:24 PM, Rausch, Felix <frausch at ipb-halle.de>wrote:

> Hi.
>
> Try to load in a .gro file of your system first. After that, use the "load
> data into molecule" option to load in the .xtc.
>
> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> Im Auftrag von shch406
> Gesendet: Mittwoch, 21. November 2012 17:47
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] Vizualization with VMD: no image appears
>
> Dear Gromacs users
>
> To visualize my trajectory with VMD I applied trjconv to .xtc trajectory
> file to eliminate water molecules and velocities remaining protein
> coordinates only.
> However, when I load this reduced file to VMD no image on screen appears,
> nevertheless VMD have identified the file as a "Gromacs compress trajectory
> file".
> What may be the cause of this?
>
> The corresponding command is as follows:
>
> trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel
>
> where MT.xtc contains ~10 frames, defau.ndx is default groups index file.
> Group 2 (Protein-H) was chosen handling dialog.
>
> Merci pour votre collaboration,
> Igor Shchechkin
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/Vizualization-with-VMD-no-image-appears-tp5003167.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>