From: [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
Subject: [gmx-users] RF-excl confusion....
Date: Wed, 05 Sep 2007 19:19:54 +0200 (MEST)
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?
The reaction-field correction applies to ALL atom pairs that are within the
cut-off
distance (or more accurately: atom pairs for which their charge group
centers
are within the cut-off distance).
So all "normal" non-bonded interaction pairs, as well as all excluded pairs
including self-pairs. The only issue is to which energy term which
contribution
is added. In old Gromacs versions the RF correction for 1-4 pairs was added
to the 1-4 energy term. In newer version it is added to the RF-excl term.
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.)?
The RF correction term is always Krf*Rij^2 - Crf, so for self pairs it is
-Crf.
Berk.
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