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.
-Justin
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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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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