[gmx-users] RF excl and protein/water potential energies
gmx3 at hotmail.com
Wed Aug 29 11:19:48 CEST 2007
>From: pascal.baillod at epfl.ch
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] RF excl and protein/water potential energies
>Date: Wed, 29 Aug 2007 11:09:10 +0200 (MEST)
>I am trying to separate potential energy contributions coming from the
>and from water in my solvated protein system.
>Dose anybody know if the term "RF excl" can be computed / written
>for protein / water atoms? I would be interested in the "RF excl"
>coming from the protein only.. Are there RF-excl corrections for
>water atom interactions also, or are they limited to the "1-4" interactions
>the protein? In the first case, I guess they would not be counted anyway,
>my rigid SPC water?
>Thanks for any info!
With reaction-field any term can not be assigned to any pair of
since reaction-field electrostatics includes a term for the reaction of the
of the system outside the cut-off. This is especially apparent in the
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
will influence the water conformation and vice versa and therefore the
are never independent.
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