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

Berk Hess gmx3 at hotmail.com
Fri Sep 4 14:53:19 CEST 2009

It contains periodic effects.
The simple way of getting this doing mdrun -rerun on the original trajectory
with a tpr file in which all charge are set to zero, except for the two ions.

But as I said, the PMF is of order 1/epsr, the direct interaction is of order 1,
if you subtract these you will get a result that is epsr (around 80!!!) times
larger than the PMF.


Date: Fri, 4 Sep 2009 16:20:40 +0400
From: ale.odinokov at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] Re: RE: question about PME

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 unneccesary?


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 effective

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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