Re: [AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD?

From: Jason Swails <>
Date: Thu, 4 Aug 2016 14:02:00 -0400

On Thu, Aug 4, 2016 at 11:27 AM, Plotnikov, Nikolay <> wrote:

> Hello,
> Is there a way to run an MD trajectory with no contributions to forces
> from solute-solvent electrostatic interactions? At the same time I want to
> keep electrostatic interactions (forces) between solute atoms and between
> solvent (thus I cannot simply kill charges neither on solute nor on solvent
> atoms).

​No. This is challenging for a few reasons. You'd need to carry multiple
pairlists (or suffer the effect of having numerous conditionals and lookups
inside inner loops) to do this efficiently, and pmemd currently does this
only for TI.

​A more serious limitation here is that there's no easy way to do this with
PME. The k-space sum is not pairwise decomposable, so you'd have to do
multiple reciprocal space sums and combine them in the correct way to
remove the effect of the interactions you had hoped to omit.

It's theoretically possible to define an energy function that at least gets
close to what you want, but few (if any) programs readily support this for
periodic simulations (and periodic boundary conditions can easily introduce
artifacts if the screening effect of solvent between solute images are


Jason M. Swails
AMBER mailing list
Received on Thu Aug 04 2016 - 11:30:02 PDT
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