[gmx-users] RF excl and protein/water potential energies

Berk Hess 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)
>Dear community,
>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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