From: Volker Knecht <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx users <gmx-users@gromacs.org>
Subject: [gmx-users] epsilon_rf
Date: Fri, 12 Jan 2007 12:04:34 +0100
Dear GROMACS users,
in the past I tended to use PME to calculate electrostatic interactions,
but to be able to reach larger timescales I would like to use reaction
field now whenever appropriate. I am wondering about an appropriate value
for the dielectric constant for a reaction field correction for simulations
of peptides in bulk SPC water or an SPC/bilayer interface. Whereas some
(group of van Gunsteren) have used the self-consistent value for SPC water
in simulations of pure SPC water, 54, most people seem to use the
experimental value of the dielectric permittivity of water at room
temperature, 78 (leading to an inconstent model). Often, authors using
reaction field do not even give the value for epsilon_rf chosen. Anezo et
al. have shown that both epsilon_rf = 54 and 80 yield similar properties
for lipid bilayer systems, and (besides PME) reaction field was one of the
recommended options for calculating electrostatic interactions for bilayer
systems. Strictly spoken, reaction field is only appropriate for a bulk
system, but it is widely used for simulations also of bilayer systems for
practical reasons. For a bilayer system, in principle, it is even less
clear which value for epsilon_rf should be chosen, since molecules in the
interface see environments with both very high and very low (close to 1)
dielectric permittivity.
I have the feeling that very different opinions on the usage of reaction
field and epsilon_rf for biomolecular simulations, ranging from rigorous to
pragmatic, coexist in the community, and it would be nice if some of you
could provide their opinion.
One can probably have long discussions one which value of epsilon_rf
one should use. But such discussions are irrelevant.
For epsilon_rf=54 the prefactor for the RF term is 0.486,
for epsilon_rf=80 it is 0.491. This difference is negligible,
especially compared to the effect that the choice of cut-off
distance will have.
If you want to avoid the discussion, use an epsilon of infinity
(prefactor 0.5), this also gives the least cut-off effects,
as the potential will be exactly zero at the cut-off.
Berk.
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