VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 13 2008 - 14:34:04 CST

Hi,
  Axel already answered this, but I thought I'd explain a bit more.

The field lines representation in VMD is based on a simple particle
advection integrator that operates on the volume gradients computed
from whatever volumetric map you have loaded (whether potential,
density, occupancy, etc).

The particle advection integrator begins by initializing field line
or stream line "seeds", which are the starting point of an integration.
Each of the seeds is selected (up to a maximum limit) based on the magnitude
of the volume gradients in the map, a maximum number of seeds, and a
"fairness" criteria that tries to prevent field lines from being
too concentrated in any one area of the volume. VMD iteratively picks
these "seeds" until these various criteria are met, and then once the
seeds have been selected, it begins the particle advection integration
for each field line, until the maximum field line length has been reached,
a critical point (a zero or huge valued gradient) is hit, or the field
line has failed to achieve a minimum linear distance from its starting
seed (e.g. some field lines will fall into an orbit surrounding a
strong source/sink with a large gradient well so they would show up as
a spiral or a "dot" rather than a field line...), and so on.

The user controls in the field lines representation provide an easy-to-use
interface for controlling most of the attributes of the visualization
that a user cares about. VMD then does all of the computational
work to satisfy the user's criteria as best it can, given the volumetric
data set that one is displaying.

Generally speaking, choosing a smaller "gradient magnitude" reduces
the number of seed points selected initially. The "minimum length" control
prevents orbiting or short spiky field lines from being drawn, requiring
that they achieve a minimum distance from their starting seed position
in order to be drawn.

Please let me know if you have more questions...
I'll try and add more information about the operation of the FieldLines
representation in the online documentation and tutorials soon.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 12, 2008 at 08:34:42AM -0500, Mary Karpen wrote:
> Does anyone know what the "GradientMag", the "Min Length", and the
> "Max Length" sliders do in the APBS plugin for VMD 1.8.6? We have
> plotted our field lines from an apbs pot.dx file, and would like to
> compare the fields of a mutant protein to the wildtype. I assume the
> "gradientmag" has something to do with the magnitude of the electric
> field in a region, but gradientmag is not a simple cutoff, because we
> find a maximum of lines somewhere in the midrange of the slider.
>
> Thanks,
> Mary
>
> Mary Karpen, Ph.D.
> Associate Professor
> Chemistry Department
> Grand Valley State University
> Allendale, Michigan 49401
> (616) 331-3778
> karpenm_at_gvsu.edu
> 

-- 
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