From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 15 2008 - 15:58:49 CDT

Hi,
  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:
  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1
  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect2

You can also color by velocity in the new alpha versions of VMD 1.8.7.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 16, 2008 at 02:10:04AM +0530, Suman Chakrabarty wrote:
> John Stone wrote:
> > Hi,
> > Just a quick note regarding velocity data for future reference...
> >
> > On Wed, Oct 15, 2008 at 12:20:33PM -0400, Axel Kohlmeyer wrote:
> > [...]
> >> vmd currently does not read or store velocity information
> >> and thus will not write it out.
> >
> > The current version of the VMD plugin API now supports velocity data and
> > the recent VMD 1.8.7 test versions will read velocity data from plugins
> > that implement support for new APIs.
>
> On a related note, if/when VMD will support velocity data, will it be
> possible to show the direction of motion of some selected particles by
> arrow in a snapshot? Is it possible now? It will be a very useful and
> interesting feature.
>
>
> --Suman.
>
>
> --
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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