VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 10 2009 - 16:28:08 CST

Hi,
  The Field Lines representation currently works by computing
a gradient map for a given volumetric dataset (e.g. electrostatic
potential map), and then computes the field lines using a simple
virtual particle advection scheme common to most algorithms of
this type. Given this, it sounds like what you'd actually want
(rather than the way this rep works now) is to compute time averaged
velocity vectors for waters associated with each grid point, and
use that as a gradient map. If we could load the gradient map
directly into VMD (perhaps with a newly written plugin), then you
could directly use that with the field lines rep. I'd say the
biggest question that remains is how best to compute the velocity
field (gradient map) in the first place. Assuming that you just
wanted something qualitative as a result, you could just take
an MD trajectory, and for each atom you could calculate what
voxels a given atom passed through between timestep A and timestep B,
and average in that effective velocity to each of the voxels visited.
Do that for all atoms and all timesteps and you ought to get something
that'd be a starting point. There're undoubtably much better methods
for computing such a velocity field (gradient map), but given the
trajectory file formats one typically has to work with, that might
be a reasonable way to start. Once one has this gradient map
in-hand, it wouldn't be too difficult to teach VMD to use that
directly for the Field Lines rep, rather than computing its own.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 10, 2009 at 05:04:23PM -0500, Roland Schulz wrote:
> Hi,
>
> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ says it is possible to
> produce Flow Fields with the Field Lines Representation. How do I generate
> the volume data with the velocities? I would like to visualize flow fields
> of water around a macromolecule.
>
> Thanks
>
> Roland
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078