From: Josh Vermaas (
Date: Wed Mar 19 2014 - 17:35:41 CDT

Hi Chola,

I think you can do what you are looking for by loading two molecules,
one with the velocity and the other with the coordinates. You'd do
something like the following:

set positionsel [atomselect coordinatemoleculenumber "water and same
residue as within 3.5 of protein"]

for { set f 0 } { $f < [molinfo coordinatemoleculenumber numframes] } {
incr f } {
#Update the frame
$positionsel frame $f
#Recalculate what is close to the protein
$positionsel update
#Since the positions and velocities have the same structure, the indices
can be shared between them
set velocitysel [atomselect velocitymoleculenumber "index [$positionsel
get index]" frame $f]
$velocitysel writepdb frame$f.pdb
$velocitysel delete

This is probably a good place to start. The biggest problem I think
you'll face is bookkeeping. The number of atoms in the selection will
change at every frame, which I've found to be a nightmare when trying to
sanely normalize my input. Another issue you'll face is that pdbs are a
particularly poor way of storing velocities, since they are a fixed
format file with not a whole lot of significant figures. For alot of
things that's fine, but I seem to remember from the last time I looked
at a velocity trajectory that the velocities come in units that mean you
are cutting off many sig figs. What I would do is calculate the quantity
of interest directly in VMD and write that to a file instead of a set of

Good luck!
-Josh Vermaas

On 03/19/2014 04:29 PM, Chola Regmi wrote:
> Dear VMD users,
> I want to write a dcd/pdb or xyz file of my selection (updated every
> frame) in each frame from my NAMD velocity dcd file. Since my
> selection is like "water and within 3.5 A of protein". But NAMD
> velocity dcd file contains only velocity components of each atoms and
> selection does not work. Is there any way VMD can be used to extract
> the velocity of selected atoms only using velocity dcd file or
> combining with trajectory dcd file.
> I want to analyse the velocity of water molecules in different
> solvation layers.
> Thank you.
> Chola