VMD-L Mailing List

From: Bryan Roessler (roessler_at_uab.edu)
Date: Wed Jun 20 2012 - 17:03:25 CDT

An example:

package require pmepot
pmepot -frames 270:275 -xscfile ../$xscfile -loadmol top -dxfile output.dx
-ewaldfactor 1.0

Cheers!

On Tue, Jun 19, 2012 at 1:06 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Tue, Jun 19, 2012 at 12:43 PM, Abolfazl Bayat
> <abolfazl.bayat_at_gmail.com> 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.
>
> axel.
>
> >
> > Cheers,
> > Abolfazl
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>