> Date: Sat, 8 Mar 2008 23:04:46 +0100
> From: [EMAIL PROTECTED]
> To: [email protected]
> Subject: Re: [gmx-users] Coul-14, LJ-14 and RF-excl definitions (2)
>
> [EMAIL PROTECTED] 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 [EMAIL
> > PROTECTED]
> > Room BCH 4121, Avenue Forel,
> > http://lcbcpc21.epfl.ch
> > CH-1015 Lausanne
> > *******************************************************************************
> > _______________________________________________
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> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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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.
> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
> _______________________________________________
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