VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Dec 02 2015 - 13:14:37 CST

Hi Ben,

 From my understanding, .vel files have the same format as the .coor
files NAMD emits. So to simply load the files into VMD isn't a big deal,
"mol addfile type namdbin blah.vel" will load the velocities of all the
atoms as though they were coordinates. This makes the structure look
like a pincushion, and usually isn't very informative. What I've done in
the past, just to get a sense of what atoms are moving quickly, is to
calculate the speed of each atom, put it into the user field, and see
what it looks like in the structure.

#Load the coordinates to localize the atoms
mol new coordinates.pdb
#Load the velocities. Your molecule will now have 2 frames, one that is
coordinates, one that is velocities.
mol addfile type namdbin blah.vel
#Set beta or user or whatever to the square of the speed.
set speedsel [atomselect top "all" frame 1]
set speedsquared [vecadd [vecmul [$speedsel get x] [$speedsel get x]]
[vecmul [$speedsel get y] [$speedsel get y]] [vecmul [$speedsel get z]
[$speedsel get z]]]
$speedsel set beta $speedquared

-Josh Vermaas

On 12/02/2015 11:42 AM, Ben Rousseau wrote:
>
> Greetings,
>
> I read this was a work in progress a few years ago, but I haven't
> found any information since then: Is there a way to load a NAMD output
> .vel file into vmd?
>
> Thank you,
>
> Ben
>