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 <[email protected]>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: [email protected] [mailto:[email protected]] > Im Auftrag von shch406 > Gesendet: Mittwoch, 21. November 2012 17:47 > An: [email protected] > 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
