From: Pawel Kedzierski (
Date: Fri Dec 12 2014 - 02:32:05 CST

W dniu 12.12.2014 o 02:47, Jun-Chieh Wang pisze:
> Among all the formats that the VMD support,
> which one should I choose if I have different total number
> of atoms for each timesteps ?
Dear Jun-Chieh,
This is as much a problem with file format as with VMD itself. It was a
design decision (for various optimizations) that VMD does not support
variable number of atoms over trajectory.
More details for example here:

That said, there is a possible workaround. You can calculate the peak
number of atoms and create trajectory file of any format which has that
surplus number of atoms constant at every frame. The atoms which should
not be visible could be placed far away and/or not shown in the
graphical representation.
You can select atoms by coordinate ranges, but you will need to update
your selection at every frame.
A more involved solution would be to store the atom presence/visibility
flag in the user fields of molecule data; I don't know if there is any
file format from which VMD load used fields but one can fill them with
> Thank you.