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It contains periodic effects.<br>The simple way of getting this doing mdrun -rerun on the original trajectory<br>with a tpr file in which all charge are set to zero, except for the two ions.<br><br>But as I said, the PMF is of order 1/epsr, the direct interaction is of order 1,<br>if you subtract these you will get a result that is epsr (around 80!!!) times<br>larger than the PMF.<br><br>Berk<br><br><hr id="stopSpelling">Date: Fri, 4 Sep 2009 16:20:40 +0400<br>From: ale.odinokov@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Re: RE: question about PME<br><br>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?<br>
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Message: 5<br>
Date: Fri, 4 Sep 2009 12:47:05 +0200<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] question about PME<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <COL113-W42988D6526BD17716CACC28EEE0@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
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This is tricky matter.<br>
<br>
The direct interaction between the ions is 1/(4 pi eps0) r (ignoring periodic effects).<br>
However, the interaction is screened by the water and therefore the effective<br>
interaction is 1/(4 pi eps0 epsr) r, where epsr is the dielectric constant of the water model.<br>
The periodic effects depend on the distance relative to the box size<br>
and they depend on the complete contents of the system.<br>
<br>
I don't understand what you want to determine exactly.<br>
<br>
Berk<br>
<br>
Date: Fri, 4 Sep 2009 14:36:30 +0400<br>
From: <a href="mailto:ale.odinokov@gmail.com">ale.odinokov@gmail.com</a><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] question about PME<br>
<br>
Hello everyone,<br>
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.<br>
Thanks in advance for your help,Alexey Odinokov<br><br>
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