AW: [gmx-users] Vizualization with VMD: no image appears
frausch at ipb-halle.de
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.
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,
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