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<TITLE>[gmx-users] Solvation Free Energy using PME</TITLE>
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<DIV> 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. </DIV>
<DIV> 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.</DIV>
<DIV> 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). </DIV>
<DIV> 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.</DIV>
<DIV> 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</DIV>
<DIV>for the chloride anion.</DIV>
<DIV>in a dielectric with</DIV>
<DIV> </DIV>
<DIV>Peter Nagy</DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV><FONT size=2>-----Original Message----- <BR><B>From:</B>
gmx-users-admin@gromacs.org on behalf of Ilya Chorny
<BR><B>Sent:</B> Tue 3/16/2004 3:02 AM <BR><B>To:</B> gmx-users@gromacs.org
<BR><B>Cc:</B> <BR><B>Subject:</B> [gmx-users] Solvation Free Energy using
PME<BR><BR></FONT></DIV><BR><BR>
<P><FONT size=2>I would like to calc the solvation free energy of a negative
ion in water<BR>using perturbation.<BR>Is it possible using PME. If I include
a counter ion it will contribute to<BR>the solvation free energy?<BR>Could I
use a reaction field instead of PME(how different will my results<BR>be?). I
tried the switching<BR>function for my long range forces but I have been
experiencing instability<BR>using the switching<BR>function. Any
recomendations would be greatly
apprecited.<BR><BR>Thanks<BR><BR>Ilya<BR><BR><BR>_______________________________________________<BR>gmx-users
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