From: McGuire, Kelly (
Date: Tue Apr 17 2018 - 13:28:19 CDT

I found a method on the VMD mailing list for coloring by velocity. I'm not sure I completely understood what was

happening though. Here is the code:

set sel_vel [atomselect 1 all]
set sel_coor [atomselect 0 all]
set nf [molinfo 1 get numframes]
for {set i 0} {$i < $nf} {incr i} {
 $sel_coor frame $i
 $sel_vel frame $i
 $sel_coor set {vx vy vz} [$sel_vel get {x y z}]

Does this take the x y z coordinates and place them in vx vy vz? Could you explain how this shows the velocity?

Also, isn't it possible to write a velocity dcd file in NAMD? If that were loaded in VMD, could I just then choose the color by velocity representation? Thanks!

Kelly L. McGuire