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To: gmx-users@gromacs.org
Subject: [gmx-users] RF excl and protein/water potential energies
Date: Wed, 29 Aug 2007 11:09:10 +0200 (MEST)
Dear community,
I am trying to separate potential energy contributions coming from the
protein
and from water in my solvated protein system.
Dose anybody know if the term "RF excl" can be computed / written
separately
for protein / water atoms? I would be interested in the "RF excl"
contributions
coming from the protein only.. Are there RF-excl corrections for
intra-molecular
water atom interactions also, or are they limited to the "1-4" interactions
of
the protein? In the first case, I guess they would not be counted anyway,
with
my rigid SPC water?
Thanks for any info!
Pascal
With reaction-field any term can not be assigned to any pair of
atoms/groups,
since reaction-field electrostatics includes a term for the reaction of the
part
of the system outside the cut-off. This is especially apparent in the
exclusion
term which even applies to the "interaction of a single charge with itself"
(see the manual), which is of course the interaction of a single charge with
the dielectric medium outside the cut-off.
It is usually anyhow meaningless to split energy contributions, since
theprotein
will influence the water conformation and vice versa and therefore the
contributions
are never independent.
Berk.
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