[gmx-developers] more on electrostatic decoupling

[hessb at mpip-mainz.mpg.de]

Quoting Michael Shirts <mrshirts at gmail.com>:

> > Michael was unclear that this is possible with the way interactions are
> > currently handled in GROMACS, but I took from Berk's suggestion that the
> > [ pairs ] section must be handled separately from the neighborlist. Can
> > someone more familiar with the code answer this definitively? That is, if I
> > specify in the [ pairs ] section an interaction between two atoms which are
> > separated by MORE than the electrostatic or vdW cutoff, will that
> > interaction still be evaluated? If so, it sounds like Berk's solution is
> the
> > way to go, as this really seems to be the best option. And if so, I could
> > use some tips on where to go in the code to modify how this pairs section
> is
> > handled (that is, to add these pair types).
>
> Berk or Erik-
>
> Could you address this part of David Mobley's question?  It seems like
> it would be necessary to send these interactions to a separate
> neighborlist that
> did not get truncated in the same way.

I think I now understand where the confusion might come from.
Some packages might do the pairs via a neighborlist.

In Gromacs all pairs are stored explicitly in the topology.
In mdrun we just loop over the list of pairs which are listed
explicitly in the .top file and have been stored in the tpr
file by grompp.

So no extra functionality is needed.
The current code would already do it, except that now one
can not specify A and B state charges seperately for pair interactions
and thus they will be perturbed when the charges are perturbed.

And for the periodicity issue.
Only the end states matter.
So one state is a fully interacting periodic system of water with solute.
The other is periodic water and a completely decoupled isolated solute.

The amount of water should be chosen large enough that the solute
has no significant effect on the periodic interactions.
Than one can take the limit to infinite water or not,
but that will not make a difference for the solvation free energy.

Berk.


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