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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