VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Feb 12 2008 - 09:53:36 CST

On Tue, 12 Feb 2008, Mary Karpen wrote:

mary,

MK> Does anyone know what the "GradientMag", the "Min Length", and the "Max
MK> Length" sliders do in the APBS plugin for VMD 1.8.6? We have plotted our

i assume you are talking about the FieldLines representation
dialog and not the APBS dialog.

MK> field lines from an apbs pot.dx file, and would like to compare the fields
MK> of a mutant protein to the wildtype. I assume the "gradientmag" has
MK> something to do with the magnitude of the electric field in a region, but
MK> gradientmag is not a simple cutoff, because we find a maximum of lines

from reading through the source code, i determined the
following:

it is a parameter that determines how many points will
act as "seeds", i.e. starting and ending points for field
lines. the slider value provides the _magnitude_ of the
field _gradient_ which is the base for the search. a point
is considered a seed, when the gradient is more than 50%
below or 50% above that value.

hope that helps,
    axel.

MK> somewhere in the midrange of the slider.
MK>
MK> Thanks,
MK> Mary
MK>
MK> Mary Karpen, Ph.D.
MK> Associate Professor
MK> Chemistry Department
MK> Grand Valley State University
MK> Allendale, Michigan 49401
MK> (616) 331-3778
MK> karpenm_at_gvsu.edu
MK>
MK> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.