From: Grace Brannigan (gracebrannigan_at_gmail.com)
Date: Wed Apr 12 2017 - 13:08:16 CDT
When building your system, you only need to consider the number of
counterions required for each end state of the transformation. In your
case, that's the same number (-1) for both molecule A & molecule B.
It gets trickier if the total charge changes over the course of the
transformation - strictly-speaking, for PME the number of counterions
should also change, then the FEP value should get corrected by the ion
solvation free energy, although in most thermodynamic cycles that
correction cancels out - but you've avoided all that.
On Wed, Apr 12, 2017 at 11:30 AM, David Huggins <djh210_at_cam.ac.uk> wrote:
> Dear All,
> I am interested in the correct way to neutralize a box in which a
> charged molecule A is mutated by FEP into a molecule B with the same
> Lets say A and B both have a charge of +1. Should counterions be added
> to neutralize just one of the charges (-1 charge added) or both
> charges (-2 charge added)?
> My guess is that the former is correct, but it may be an issue that
> the decoupled atoms interact with their periodic images. Does
> alchDecouple then need to be set to off?
> Dr David J. Huggins
> University of Cambridge
> Department of Chemistry
> Lensfield Rd
> CB2 1EW
> United Kingdom
> Phone: +44 (0)1223 763854
> Email: djh210_at_cam.ac.uk
> Web: http://huggins-lab.tcm.phy.cam.ac.uk/
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