[gmx-users] RF-excl confusion....

[pascal.baillod at epfl.ch]

Dear community,

Thanks for your kind answer, Berk! I am actually trying to understand the
"RF-excl" term, which comes from one of your contributions to version 3.3.:

http://www.gromacs.org/content/view/18/132/

If you will, I have a couple of perhaps naive questions:

1) 2 sentences appear to be in contradiction, to me:

a) The sentence "The 1-4 energies are now reported without reaction-field
correction.", that I cite from the web page above, describing the RF-excl
feature, and

b) "The reaction-field correction should also be applied to all excluded atoms
pairs, including self pairs, in which case the normal Coulomb term in eqns. 4.12
and 4.16 is absent.", that I cite from the manual of version 3.3, page 45.
 
If I understand well, ecluded atom interaction pairs are selfinteracting atoms
or 1-4 interacting atoms. These sentences would mean that the reaction field
correction is applied to the former but NOT to the latter?

2) I don't exactly understand the "self pair" of the sentence I cite in 1 a). To
compute a self pair interaction, we would obtain i=j in rij of equations 4.12
and equation 4.16 of the same manual page, making Vcrf and Fi equal to zero. How
could one then apply any reaction-field correction, as suggested in the sentence
cited in 1 a)?

3) Is the RF-excl term equal to the reaction field correction "Krf*Rij^2 - Crf"
of eq. 4.13., or to the constant Crf (eq 4.15.)?

I thank you very much for any info!

Regards,

Pascal
















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Pascal Baillod (PhD student) 
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