[gmx-users] RF-excl confusion....

[Berk Hess]

>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 confusion....
>Date: Wed, 05 Sep 2007 19:19:54 +0200 (MEST)
>
>
>Dear community,
>
>Thanks for your kind answer, Berk! I am actually trying to understand the
>"RF-excl" term, which comes from one of your contributions to version 3.3.:
>
>http://www.gromacs.org/content/view/18/132/
>
>If you will, I have a couple of perhaps naive questions:
>
>1) 2 sentences appear to be in contradiction, to me:
>
>a) The sentence "The 1-4 energies are now reported without reaction-field
>correction.", that I cite from the web page above, describing the RF-excl
>feature, and
>
>b) "The reaction-field correction should also be applied to all excluded 
>atoms
>pairs, including self pairs, in which case the normal Coulomb term in eqns. 
>4.12
>and 4.16 is absent.", that I cite from the manual of version 3.3, page 45.
>
>If I understand well, ecluded atom interaction pairs are selfinteracting 
>atoms
>or 1-4 interacting atoms. These sentences would mean that the reaction 
>field
>correction is applied to the former but NOT to the latter?
>

The reaction-field correction applies to ALL atom pairs that are within the 
cut-off
distance (or more accurately: atom pairs for which their charge group 
centers
are within the cut-off distance).
So all "normal" non-bonded interaction pairs, as well as all excluded pairs
including self-pairs. The only issue is to which energy term which 
contribution
is added. In old Gromacs versions the RF correction for 1-4 pairs was added
to the 1-4 energy term. In newer version it is added to the RF-excl term.

>2) I don't exactly understand the "self pair" of the sentence I cite in 1 
>a). To
>compute a self pair interaction, we would obtain i=j in rij of equations 
>4.12
>and equation 4.16 of the same manual page, making Vcrf and Fi equal to 
>zero. How
>could one then apply any reaction-field correction, as suggested in the 
>sentence
>cited in 1 a)?
>
>3) Is the RF-excl term equal to the reaction field correction "Krf*Rij^2 - 
>Crf"
>of eq. 4.13., or to the constant Crf (eq 4.15.)?

The RF correction term is always Krf*Rij^2 - Crf, so for self pairs it is 
-Crf.

Berk.

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