VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Feb 26 2011 - 15:50:57 CST

On Sat, Feb 26, 2011 at 4:02 PM, Robin Varghese <rvarghese_at_vbi.vt.edu> wrote:
> Hello,
> I have a pot.dx file from running APPBS through VMD.  When I open the pot.dx file through my text editor I see three columns.  What do each column of numbers represent.  I am trying to compute the electrostatic surface potential.  Can you please help?

robin,

the fact that you see three columns has no relevance. it could be five
or ten and it
would not change anything. each number is the value of the
electrostatic potential
in space at a grid point that is described through the grid
description in the header.
it basically tells you how the data on a multi-dimensional grid is
mapped to a one
dimensional list.

here is the blurb from the dx file reader in VMD that may be helpful:

/* DX potential maps
 *
 * Format of the file is:
 * # Comments
 * .
 * .
 * .
 * object 1 class gridpositions counts xn yn zn
 * origin xorg yorg zorg
 * delta xdel 0 0
 * delta 0 ydel 0
 * delta 0 0 zdel
 * object 2 class gridconnections counts xn yn zn
 * object 3 class array type double rank 0 items { xn*yn*zn } [binary]
data follows
 * f1 f2 f3
 * f4 f5 f6 f7 f8 f9
 * .
 * .
 * .
 * object "Dataset name" class field

 * Where xn, yn, and zn are the number of data points along each axis;
 * xorg, yorg, and zorg is the origin of the grid, assumed to be in angstroms;
 * xdel, ydel, and zdel are the scaling factors to convert grid units to
 * angstroms.
 *
 * Grid data follows, with a single or multiple values per line (maximum
 * allowed linelength is hardcoded into the plugin with ~2000 chars),
 * ordered z fast, y medium, and x slow.
 *
 */

"electrostatic surface potential" is a very vague description in this context.
what kind of surface, where. and how do you determine the surface?
the more precise you describe your problem and why you want to compute
what, the easier it is for other people to help.

axel.

> Thanks,
> Robin
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.