[gmx-users] Solvation Free Energy using PME
Nagy, Peter I.
PNAGY at UTNet.UToledo.Edu
Tue Mar 16 14:17:01 CET 2004
I think that this is an interesting problem. I am not an experienced GROMACS user, and my remark would rather refer to a more thereoretical point. The question depends on the definition of the solvation free energy.
If you want to see the free energy difference between a gaseous and an in-solution anion, then I think NO counterion should be added to the solution model. I presume that the free energy calculation would be performed by annihilation of the anion in the solvent. If the counterion is present then the anion-cation interaction will be ceased, which would have a large effect on the calculated value.
The corresponding physical procedure would be that the anion is being formed in the gas phase and enters the solvent without grabbing a cation, also necessarily encountering in the gas phase. This is difficult to perform technically, and I believe that the experimental values are determined by indirect procedures. You may want to consult the paper of Pearson (J.Am.Chem. Soc., 1986, 108, 6109) and that of Rossinsky (Chem. Rev., 1965, 65, 467).
So I think that no counterion should be considered. In this case, the Ewald in GROMACS may not work properly. But since a single anion in a solvent is not a real physical system (except under very special technical conditions), if one uses Ewald one would calculate anion-anion repulsive interactions without considering anion-cation attractive interactions, generally present for a real system.
For such a case, Jorgensen et al. (Chem. Phys., 1989, 129,193) used a cutoff and the Born approximation in Monte Carlo simulations. The Born radius was set to the cutoff. Good result was obtained
for the chloride anion.
in a dielectric with
From: gmx-users-admin at gromacs.org on behalf of Ilya Chorny
Sent: Tue 3/16/2004 3:02 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Solvation Free Energy using PME
I would like to calc the solvation free energy of a negative ion in water
Is it possible using PME. If I include a counter ion it will contribute to
the solvation free energy?
Could I use a reaction field instead of PME(how different will my results
be?). I tried the switching
function for my long range forces but I have been experiencing instability
using the switching
function. Any recomendations would be greatly apprecited.
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