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Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
Subject: [gmx-users] RF-excl confusion (2)....
Date: Thu, 06 Sep 2007 22:38:30 +0200 (MEST)
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.?
That is completely incorrect.
I forgot in which version things changed.
But in the "older" versions the RF correction (energy and force) was added
to all non-bonded pairs
and to 1-4 pairs (which are in the exclusion list), but not to other
exclusions.
The RF correction for 1-4 pairs was in the 1-4 energies.
Currently all pairs within the cut-off have the excl correction (as it
should be).
The energies are in:
non-bonded: Coul-SR and Coul-LR if present
1-4: RF-excl (not in the 1-4 energy term, that has only the pure Coulombic
term).
other excluded pairs, including self-pairs: RF-excl
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?
You can NOT term these contributions "self-pair interactions".
An atom does not interact with itself.
From which pairs, solvent or protein, the RF-excl term comes depends on your
system.
But again, ANY RF contribution can not be assigned to the atom pair
that it is calculated for. Any contribution is a collective effect of
all charges within the cut-off sphere with the dielectric around it.
Please read some literature on reaction-field electrostatics.
It would be more correct to also add the RF correction for all non-bonded
atom pairs to the RF-excl term instead of to the Coulomb energy.
But that would lead to a lot of noise in the Coulomb energy term due to
cut-off effects
(and would require some changes in the assembly innerloops).
Berk.
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