From: Axel Kohlmeyer (
Date: Tue Jun 19 2012 - 13:06:38 CDT

On Tue, Jun 19, 2012 at 12:43 PM, Abolfazl Bayat
<> wrote:
> Dear vmd users,
> I am trying to use PMEpot plugin for calculating the electrostatic potential
> of my structure (protein+membrane+water). I need this potential for any
> frame of my DCD file.
> My questions are as following:
> 1- How can I calculate the electrostatic potential for all frames?

do you mean averaged over them, or individually?
the first option is supported by the GUI, the second
requires you to write a small script and use the text
mode interface of the plugin.

> 2- How can I interpret the numbers in the outfile DX file? There are
> three columns there but I if we assign potential for each point in space we
> need four numbers (three coordinates + one potential).

nope. the number of columns has no meaning.
each number is a data point on a regular grid.
the three coordinates are inferred from the
definition of the grid in the preceding parts
of the .dx file.


> Cheers,
> Abolfazl

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.