From: Bjoern Olausson (
Date: Tue Jul 06 2010 - 02:51:24 CDT

On Monday 05 July 2010 22:59:22 Ardy Davari wrote:
> Hi,
> Are there any scripts available to color a charmm dcd/psf by kinetic
> energy?
> If not, what's the best way to go about producing one?
Since the energy is not stored in the dcd you have to either calculate it or
get it elsewhere.

If you want to color it by the TOTAL energy you could simply grep the TOTAL
(TOTAL2, TOTAL3) from the NAMD log file for every frame and write it to a file
(You might want to check the build in extension "NAMD Energy"). Then write a
little script that colors every frame of you dcd by a certain color depending
on the TOTAL energy.

set sel [atomselect top "all"]
for {set i 0} {$i < $maxFrames} {incr i} {
    $sel frame $i
    $sel set user $YourEnergyRepresentationValue

I don't know how to read in an external file but I am sure someone else does,
or you can figure it out by yourself.

Hope this helps.


Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942