Hi,
The RF correction is NOT applied to 1-4 pairs.
It is applied to excluded pairs, independently of it they interact via 1-4
interaction or not.
For RF simply all atom pairs in a cut-off sphere need to be corrected.
The simplest way of doing this is correcting the non-bonded potential
and correcting all pairs that do not interact via the non-bonded potential
(excluded pairs).
For why one has to correct all pairs with an r^2 function, you have to read the
literature.
Berk.
> To: gmx-users@gromacs.org
> Date: Wed, 12 Mar 2008 16:26:05 +0100
> From: [EMAIL PROTECTED]
> Subject: [gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)
>
> Dear developers,
>
> I would again like to thank David, Xavier and Berk for their very informative
> explanations on RF-excl and 1-4 interactions. I am still a bit confused,
> though,
> with Berk's very last statement on this issue. If I quote it:
>
> "The reaction field is not applied to pair (1-4) terms. Therefore there are no
> issues with fudgeQQ."
>
> As far as I understood, the reaction field correction IS applied to (1-4)
> pairs,
> but added to the RF-excl term, and not to Coul-14 term. At least this is what
> I
> understood from another explanation from Berk, sent on the mailing list
> sometime
> around September 2007:
>
> "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 cutoff distance). So all "noraml non-bonded interaction
> pairs, as well as all excluded pairs including self -pairs. The only issue is
> to
> which energy term wich contribution is added. In old Gromacs versions the RF
> correction for 1-4 pairs was added to the 1-4 energy term. In the newer
> version
> its added to the RF-excl term."
>
>
> I would also like understand why the reaction field correction is applied to
> excluded atom pairs. The corrected coulomb potential described in the manual
> reads (please open the attached pdf for the compiled equations):
>
> V_{crf} = f *q_i *q_j [ \frac{1}{r_{ij}} + k_{rf}r^2_{ij} - c_{rf} ] (1)
>
> This is equivalent to
>
> V_{crf} = V_c + V_{rf} (2)
>
> where V_c is the usual Coulomb potential energy, and V_{rf} is the
> reaction field correction.
>
> For excluded atom pairs, there is no Coulomb interaction, except for 1-4
> pairs,
> where there is a reduced Coulomb interaction. However, in agreement with what
> I
> state above, the code dose seem to compute a reaction field correction for all
> excluded atom pairs. In the RF_excl_correction routine of mdlib/rf_util.c,
> this
> correction reads:
>
> V_{rf} = f q_i q_j ( k_{rf}r^2_{ij} - c_{rf} )
>
> That means we apply a potential that is a function of r^2, yielding a force
> whose magnitude increses with r and whose direction is opposed to the Coulomb
> force !!! What is the physical justification to V_{rf} in the absence of V_c
> for excluded pairs?
>
> I thank you very much for your help!
>
> Pascal
>
>
> *******************************************************************************
> Pascal Baillod (PhD student)
> *******************************************************************************
> Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
> Laboratory of Computational Chemistry and Biochemistry [EMAIL
> PROTECTED]
> Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
> CH-1015 Lausanne
> *******************************************************************************
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