Re: [AMBER] Calculating electrostatic potential in cpptraj

From: Jason Swails <>
Date: Sat, 16 Aug 2014 21:05:24 -0400

On Sat, Aug 16, 2014 at 4:20 PM, Covington, Cody Lance <> wrote:

> Thanks Jason
> >> Hello all
> >>
> >> Is there a way to calculate the electrostatic potential at a given
> >> atom position or point in space in cpptraj?
> >
> >
> >cpptraj cannot (yet) do PME electrostatics. There are a couple actions
> that do electrostatic
> >calculations, but they do direct space pair-pair interactions only using
> minimum image convention.
> >
> What are the methods to calculate through the direct space sum?

​The "pairwise" and "lie" actions compute electrostatic and van der Waals
interactions (as does the 'spam' action). I think only "pairwise" will
really give you what you want.

> >
> >>
> >> Or any other analysis program?
> >>
> >
> >None in Amber that I know about.
> >
> >
> >>
> >> I can calculate it using my own programs, but I want to use PME to get
> >> long range electrostatics that would go beyond where periodic
> >> boundary conditions end. This might seem silly, but I have a
> >> surfactant system that has a high ionic strength.
> >>
> >>
> >
> >
> >>
> >>
> >> I have also tried to use
> >>
> >> image xoffset 0 yoffset 0 zoffset 0
> >>
> >> image xoffset 0 yoffset 0 zoffset 1
> >>
> >> ... etc
> >>
> >> To make the system more like and 'infinite' one, but this is quite
> >> cumbersome.
> >>
> >
> >It will be _very_ hard to make the system large enough that you can
> compute an electrostatic potential
> >using just a direct sum-over-pairs (and it will get _very_ slow very
> quickly). Your best bet really is
> >to use an Ewald-based method. There are a couple options:
> I have done some tests and I think I can use the direct space sum if I can
> get about 20 nm between my structure and the boundary. The potentials are
> different but the fields are about the same.

Well the field strength drops off as 1/r^2, whereas the ESP varies as 1/r,
so that would make sense. But you had said you wanted the electrostatic
potential, not the electric field. And the field is easier, anyway -- just
compute the electrostatic force at a particular point and divide by the
charge (no need to take any kinds of differences to isolate the ESP at a
single point from an energy).

Thanks for the suggestions, I also wondered if I could somehow use amber's
> PME code somehow?

I suppose so -- calculating the ESP may actually be easier with Amber now
that I think about it so long as you can add the dummy particle (but
calculating the electric field I think would be harder). You'll need to
create an additional topology file with the extra dummy particle (assuming
you want the ESP and not just the electric field). ParmEd _can_ be used to
add the extra particle, but it would probably be easier to use tleap.

Then compute the energy using sander or pmemd using a single-point energy
calculation. Extract the electrostatic energy (EEL and the 1-4 EEL values
added together) from the output file and take the difference in the way I
described before.

The electric field would be harder to get, since you would need to get
_just_ the electrostatic force (which is not decomposed like the energy is
in the output file). You would need to use ParmEd to zero-out all of the
bond, angle, torsion, and Lennard-Jones terms, then compute and print the
force for each particle using the "ntwf" variable.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Aug 16 2014 - 18:30:02 PDT
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