Well. I tried with VMD. It only showed 3 frames of my trj file. Then I switched to OVITO with same file and it did show all the 1000 frames.
if you check your VMD console terminal you should see that VMD is telling you that the number of atoms changed and it stopped reading.
the way how VMD reads and stores trajectories does not allow for trajectories with a varying number of atoms or changes in the topology in general, as that information is only stored only once for efficiency reasons and being able to visualize and process very long trajectories of very large biological systems. there are multiple workarounds each with their own set of limitations.
axel.