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

Rausch, Felix frausch at
Wed Nov 21 17:54:28 CET 2012


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 [mailto:gmx-users-bounces at] Im Auftrag von shch406
Gesendet: Mittwoch, 21. November 2012 17:47
An: gmx-users at
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:
Sent from the GROMACS Users Forum mailing list archive at
gmx-users mailing list    gmx-users at
* Please search the archive at before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at
* Can't post? Read

More information about the gromacs.org_gmx-users mailing list