From: Bryan Roessler (
Date: Thu Oct 27 2011 - 11:34:40 CDT


Due to the size of my system, I am forced to break my rmsd analysis into
chunks, run the script on our high-throughput cluster, and finally recombine
the data into a formatted tml file. However, due to the requirements of the
timeline plugin, I am forced to load all of the analyzed frames of my
trajectory before I can load my pre-rendered tml file. Due to memory
limitations, this is impossible. I am only interested in visualizing the
data using the "heat map" featured in the timeline plugin and do not care if
my residue selections are passed to the structure viewer.

Is there anyway to visualize the data in VMD without having to load the
corresponding trajectory files first? If not, does anyone have any
recommendations for programs that will be able to generate a good visual
representation of the change in rmsd values by residue over simulation time?
I can obviously tweak my script to generate the appropriate formatting so
that the file can be natively imported into the recommended program.


Bryan Roessler
The University of Alabama at Birmingham