[gmx-users] switching function and NPT

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Tue Mar 16 18:36:02 CET 2004

Hello I would like to calculate the solvation free energy of ions. In
order to do so I must use a switching function or a reaction field. I
Prefer the switching function by I notice that is very unstable  when I
use it with the pressure coupling. Has anyone else noticed this or used 
The switching function and if so what were your parameters?
-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of Nagy, Peter I.
Sent: Tuesday, March 16, 2004 5:14 AM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Solvation Free Energy using PME
Dr. Ilya Chorny                                            Department of
Pharmaceutical Chemistry
DOE/SLOAN Postdoctoral Researcher       University of California, San
Tel:  (415)-476-6875                                   600 16th st
Fax:  (415)502-4222                                    San Francisco, CA
Cell: (408)887-8496
                                   Email: ichorny at maxwell.ucsf.edu
     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
Peter Nagy
-----Original Message----- 
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
using perturbation.
Is it possible using PME. If I include a counter ion it will contribute
the solvation free energy?
Could I use a reaction field instead of PME(how different will my
be?). I tried the switching
function for my long range forces but I have been experiencing
using the switching
function. Any recomendations would be greatly apprecited.



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