VMD-L Mailing List

From: Abolfazl Bayat (abolfazl.bayat_at_gmail.com)
Date: Tue Jun 19 2012 - 11:43:42 CDT

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?
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).

Cheers,
Abolfazl