Re: [AMBER] Negative interaction energy between Sodium ions?

From: David Cerutti <>
Date: Mon, 14 Nov 2016 17:46:16 -0500

I'm trying to envision exactly what you are doing; it seems simple enough:
a collection of sodium ions left over after removing the water and DNA to
which the sodium particles were counterions. My feeling is that there is
something in the way the Particle Mesh Ewald's tinfoil boundary conditions
that's creating the non-intuitive energy you see. If you like, I have a
Matlab program that computes the Particle-Mesh Ewald sum for a collection
of atoms with partial charges. You will make an array crdq with the format:

crdq = [
  x1, y1, z1, q1;
  x2, y2, z2, q2;
  xN, yN, zN, qN

And then supply necessary information like the box size, grid density, and
other factors that you can read from the comment explanations preceding
each function (it works with the typical Matlab help <funcname> feature).
It will return the total energy and you can then dissect it however you
want by reaching into the Matlab functions themselves and pulling out more
variables, but the functions return a good amount of detail as written.
For instance, if you look in the reciprocal space calculation, the first
thing that happens is that the (0,0,0) array element of the frequency
transformed mesh gets set to zero, effectively clipping off any excess
charge on the system.

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Received on Mon Nov 14 2016 - 15:00:02 PST
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