problem with flying atoms in Si crystal

Don’t know - that’s a VMD question.


a very simple option to work around the VMD issue is to either use a different viz program
or open the dump file only after the atoms have flown off. that part of the simulation is
pointless and would be considered equilibration in any case.

if you are really hardnosed about showing everything in your trajectory, then you
can dump to an .xyz file and use the workaround for xyz files in topotools:—documentation#TOC-readvarxyz-file-name-