[gmx-users] RF-excl confusion (2)....

[pascal.baillod at epfl.ch]

Dear community,

Thanks again for these most helpful explanations, Berk! If I understood
everything correctly, the following questions could be answers..

1) I would like to know why the RF correction of 1-4 interacting atoms was
counted in another term, RF-excl. If I understand well, it is not correct to add
this interaction to the total potential energy of atoms, from which atomic
forces will be derived, since 1-4 electrostatic interactions are too strong. So
the RF-excl term would just be a control and is added to no potential energy at
all? If it is added, in what way is that done differently than in versions older
than 3.3.?

2) The RF-excl term is an addition of all excluded pair interactions, from the
solvent and from the protein. I guess the biggest part of the RF-excl term would
come from the solvent self pair interactions, in this case?

Thank you very much for your patience!

Best regards,

Pascal


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Pascal Baillod (PhD student) 
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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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