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

Justin Lemkul jalemkul at vt.edu
Wed Nov 21 17:53:37 CET 2012

On 11/21/12 11:45 AM, shch406 wrote:
> 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?

You need to load a matching coordinate file (.pdb, .gro, etc) first and then 
load the trajectory as data for it.  The contents of the coordinate file and 
.xtc must match; if there is a different number of coordinates in each, then VMD 
will fail to load the trajectory properly.


> 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.


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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