From: JeJoon Yeon (
Date: Sun Jul 26 2015 - 22:17:10 CDT


I have a xyz format file, made up of total 1000 frame and 1761 atoms per a

For the visualization & post processing purpose, I swapped several atom's
name to the different kind, to distinguish their position and movement
under specific conditions.

The position and number of those swapping atoms are different among frames
to frames. For example, atom #1 can be swapped in first frame, but atom #20
and #100 can be swapped (while #1 is replaced to original) in the next

After the swapping, when I command vmd -xyz, something weird
happened. I can't see any of swapped atoms. I changed some Si atoms to Al
or Mg, but none of Al or Mg were detected during entire frames. I changed
some O atoms to N and F, but only N is visible, no F were detected.

More strange thing is, single frame or 10 frame file (which was swapped)
looked perfectly okay. I can see all swapped atoms there. However, only
1000 frame or 10000 frame files made those problems - swapped Al, Mg, He,
F... atoms were not visible.

How can I escape from this situation? I really want to show those different