Re: [AMBER] cpptraj LIE on a ghost-atom

From: Jason Swails <>
Date: Thu, 22 Dec 2016 16:34:27 -0500

On Wed, Dec 21, 2016 at 9:45 AM, Elisa Pieri <>

> Dear Amber users,
> I would like to get the electrostatic energy value in a point that is NOT
> occupied by an atom. I've been using the LIE function in cpptraj for other
> "real" atoms, but the only chance I see to continue using it in this case
> is modifying the parm file inserting a "ghost atom" or changing some other
> atom coordinates (and I really would like to avoid that).
> Can you help me? Thanks in advance.

​Electrostatic energy is always between two charged particles. What you
describe is an electrostatic potential, or voltage. This can be computed
either by looping over all particles and computing

k*q/r, where q is the charge of that atom and r is the distance between
that atom and your point of interest (and k is the electrostatic
constant). You could write a script to do this by hand. An alternative is
to create a dummy atom at that point with a charge of 1 coulomb. Then you
can compute the electrostatic energy of that dummy atom and divide by its
charge (which is just 1).

In both cases, you'll need to do a little bit of scripting (although there
may be a tool that can be used to calculate the ESP at a point, but I can't
recall one off the top of my head).


Jason M. Swails
AMBER mailing list
Received on Thu Dec 22 2016 - 14:00:02 PST
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