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.
Berk
Date: Fri, 4 Sep 2009 16:20:40 +0400
From: [email protected]
To: [email protected]
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 <[email protected]>
Subject: RE: [gmx-users] question about PME
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
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.
Berk
Date: Fri, 4 Sep 2009 14:36:30 +0400
From: [email protected]
To: [email protected]
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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