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

[Berk Hess]

>From: pascal.baillod at epfl.ch
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>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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