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

[Berk Hess]

> Date: Sat, 8 Mar 2008 23:04:46 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Coul-14, LJ-14 and RF-excl definitions (2)
> 
> pascal.baillod at epfl.ch wrote:
> > Dear developers, 
> > 
> > Could somebody please tell me if I understood the following correctly (if the
> > statements below are correct in gromacs)?
> > 
> > Excluded bonded at pairs:
> > 
> > Pairs i to i+1   No non-bonded terms, all in bonded terms?
> > Pairs i to i+2   No non-bonded terms, all in bonded terms?
> > Pairs i to i+3   No non-bonded terms, all in bonded terms?
> > Pairs i to i+4   Coul-14 to account for bonded i to i+4 interaction?
> >                  LJ-14 to account for bonded i to i+4 interaction?
> 
> This can be confusing. If you set nrexcl in your topology to 3 (default 
> in pdb2gmx generated topologies) this is correct. In addition you have 
> dihedral terms for 1-4 interactions of course. If you set nrexcl 
> differently the effect will be different, and if you choose to list 1-3 
> interactions under the pairs section they will be computed.
> 
> 
> > 
> > Rf-excl : Reaction field correction "Krf*Rij^2 - Crf" for ALL excluded at pairs
> > mentioned above? 
> For everything in the exclusion list, independent of pairs. I'm not sure 
> whether the Rf-excl correction takes fudgeQQ into account.

The reaction-field is not applied to pair (1-4) terms.
Therefore there are no issues with fudgeQQ.

Berk.

> > 
> > For non bonded at pairs, the reaction field correction is included in the
> > Coul-SR and Coul-LR terms?
> Yes.
> 
> 
> 
> 
> > 
> > I would also like to thank David van der Spoel and Xavier Periole for their very
> > helpful information on protein-solvent interaction energy, bringing answers
> > beyond expectation to my previous question!!
> > 
> > Thanks a lot !!!
> > 
> > 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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> 
> 
> -- 
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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