# [gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)

pascal.baillod at epfl.ch pascal.baillod at epfl.ch
Wed Mar 12 16:26:05 CET 2008

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

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

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

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Pascal Baillod (PhD student)
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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	pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne
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