From: Ardy Davari (
Date: Wed Jun 16 2010 - 12:04:04 CDT


Is it possible to color by speed of an atom using a charmm35 psf and dcd
file? I came across the post attached below, and I am not sure how to do
this in 1.8.7.

Best Regards,

Ardy Davarifar

****Attached post ***

  One can do that in the test versions of VMD 1.8.7 now, with a script,
by querying the atom velocity components and drawing an arrow for each
of the atoms of interest. The new velocity component keywords are
"vx", "vy", and "vz". You can do something like:
  set sel [atomselect top "index 1 to 5"]
  set coords [$sel get { x y z }]
  set velocities [$sel get { vx vy vz }]
...normalize the velocities to some scale...
...draw the arrow from the coordinate to an endpoint calculated by
   adding the scaled velocity vector to the coordinate...

See Axel's tutorial on various customized drawing commands,
and dynamically updating graphics:>>

You can also color by velocity in the new alpha versions of VMD 1.8.7.
  John Stone<>