From: Anthony Ruth (
Date: Fri Nov 22 2019 - 09:07:31 CST

Hello, I make videos of kinetic monte carlo simulations with VMD. My
current process results in an enormous amount of disk space being used and
a lot of time spent writing structure files and reading them. I would like
to speed up this process by making the kmc produce more compact structure
files which are compatible with VMD. I tried looking through the list of
supported file types in VMD, but it was overwhelming and I am hoping to get
some advice on a good filetype to use.

The biggest waste in my current setup is that few atoms move each frame but
all of the atoms are repeated in the file for every frame. For example, the
first frame is given by an .xyz file. The next frame has only the changes
relative to the first frame, e.g. atom1 moved to (5,3,0) atom5 moved to
(4,4,0). Is there a filetype or a combination of filetypes that VMD could
interpret this kind of information from and would obtain the same set of
frames as printing a full structure for each frame?

The other option I as looking at is a simple binary encoded format. Do you
have a recommendation on a commonly used binary format?

Anthony Ruth
Condensed Matter Theory
University of Notre Damee