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

shch406 shch406 at bpci.kiev.ua
Wed Nov 21 17:45:19 CET 2012

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
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

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