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

Berk Hess gmx3 at hotmail.com
Wed Mar 12 16:40:16 CET 2008


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.


> To: gmx-users at gromacs.org
> Date: Wed, 12 Mar 2008 16:26:05 +0100
> From: pascal.baillod at epfl.ch
> 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	pascal.baillod at epfl.ch
> Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
> CH-1015 Lausanne	
> *******************************************************************************

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