VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 17 2017 - 11:10:03 CDT
The APBS program generates a so-called "DX" file that contains
a scalar field, where the electrostatic potential is listed for each
grid point on a uniform grid. You can read and interpret the DX
file in your own code if you want to do analysis on it. From your
question it was unclear if you wanted to evaluate potentials relating
to the isosurface mesh computed by VMD, or if you just wanted the
APBS electrostatic field in the DX file. By definition, the vertices of
the triangles in the isosurface mesh computed by VMD lie on points that
have the same electrostatic potential. Since these points may fall
in-between the uniformly-spaced grid points determined by APBS, they
are found through trilinear interpolation within VMD as part of the
Marching Cubes algorithm. I assume therefore, that you really want
to analyze the DX file written by APBS, and not the isosurface
mesh produced by VMD.
On Fri, Mar 17, 2017 at 08:53:37AM +0100, horst_at_lillig.de wrote:
> Dear fellows,
> I would like to extract some numerical data from the electrostatic calculations, computed using the APBS extension.
> Mostly, I'd be interested to extract numerical data for further calculations regarding the visualization in form of isosurfaces [-1/+1].
> Is there a way to extract these, e.g. in form of x,y,z coordinates + charge?
> Thank's in advance, Christopher Horst Lillig
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/