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

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 8 23:04:46 CET 2008

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.
> For non bonded at pairs, the reaction field correction is included in the
> Coul-SR and Coul-LR terms?

> 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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