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 [EMAIL PROTECTED]
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] 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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