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

[Xavier Periole]

Just to make sure there is no confusion, at that point I am confused!
>> Excluded bonded at pairs:
>> 
>> Pairs i to i+1   No non-bonded terms, all in bonded terms?
those are bonds
>> Pairs i to i+2   No non-bonded terms, all in bonded terms?
those are angles
>> Pairs i to i+3   No non-bonded terms, all in bonded terms?
those are dihedrals
>> 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?
those are just regular non-bonded interactions.

The 1-4 interactions belong to the i-i+3 interactions, isn't it?
There is a dihedral and a "special" LJ.

This is explained in page 71 of the manual 3.3 (probably 3.3.0).
> 
> 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?
> 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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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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