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

From: Elisa Pieri <>
Date: Tue, 3 Jan 2017 12:36:25 +0100

Thank you very much Jason,

I'm trying to understand (without much success) from to manual what is the
best way to insert a dummy atom. What I have is the parameter file and a
.nc file (20000 frames). Can I modify the trajectory file (knowing the
coordinates of the dummy atom in each frame)? What tools should I use, do
you have a strategy, to suggest?

Thank you for your time,

On Thu, Dec 22, 2016 at 10:34 PM, Jason Swails <>

> On Wed, Dec 21, 2016 at 9:45 AM, Elisa Pieri <>
> 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 Tue Jan 03 2017 - 04:00:03 PST
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