On Wed, Dec 21, 2016 at 9:45 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> 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).
HTH,
Jason
--
Jason M. Swails
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Received on Thu Dec 22 2016 - 14:00:02 PST
