[gmx-users] Re: RE: question about PME

Alexey Odinokov ale.odinokov at gmail.com
Fri Sep 4 14:20:40 CEST 2009

We wish to withdraw the direct interaction between the ions and learn how it
appears in the computed PMF profile. As a true Coulomb value? Or as its
Ewald counterpart contaminated by periodic effects? In the latter case we
are looking for the pertaining correction. Is it available? Or is it


Message: 5
Date: Fri, 4 Sep 2009 12:47:05 +0200
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] question about PME
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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This is tricky matter.

The direct interaction between the ions is 1/(4 pi eps0) r (ignoring
periodic effects).
However, the interaction is screened by the water and therefore the
interaction is 1/(4 pi eps0 epsr) r, where epsr is the dielectric constant
of the water model.
The periodic effects depend on the distance relative to the box size
and they depend on the complete contents of the system.

I don't understand what you want to determine exactly.


Date: Fri, 4 Sep 2009 14:36:30 +0400
From: ale.odinokov at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] question about PME

Hello everyone,
We calculate the potential of mean force (PMF) for the ion pair AB (the
solute) in a solvent. The computation is made in terms of the COM pulling.
The PMF includes both the solute-solvent and intrasolute interactions. We
are interested only in the solvation energy, i. e. the electroststic
interaction between A and B must be eliminated from the PMF. The question
is, whether we have to subtract the true Coulomb energy 1/R (R is the
inter-ionic distance) or this term is distorted during the PME computation
and must be modified in some way before being subtracted.
Thanks in advance for your help,Alexey Odinokov
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