[gmx-developers] more on electrostatic decoupling

[hessb at mpip-mainz.mpg.de]

Quoting Michael Shirts <mrshirts at gmail.com>:

> > 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.
>
> But HOW are the pairs interactions that are listed in the topology
> calculated?  By the -nonbonded- part of the code, like the 1,4's?  So
> that the PME calculations have nothing to do with it? I think that's
> the real question.

What I mean is the [ pairs ] section in the .top file,
which is normally only used for 1-4 interactions.

In mdrun do_nonbonded14 takes care of this.
There a neighborlist of one atom pair is made
and the proper LJ parameters and charges are set.

I can implement the three extra pair type interactions
that I mentioned before.
Then you can already do a simulation by adding the pairs
and exclusions by hand in the .top file.

Berk.



>
> > 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.
>
> So . . . what we want is the explicitly stated pair energies to remain
> constant when the Coulombic interactions with the REST of the system
> are changed, correct?
>
> > 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.
>
> I'm not entirely sure that we have a handle on this -- it would be
> good to put some rigourous (i.e., not just handwaving) bound on this.
>  The ligand-ligand interactions are the same reguardless of the
> solvent, but presumably, there is some effective screening by the
> solvent molecules.  What this screening actually results in probably
> involves the boundary conditions at infinity.
>
> The other problem is, of course, the free energy of charging the vapor
> states.  For ligand binding, the charging of the ligand in the two
> simulations (decharging in presence of solvent, decharging in the
> presence of solvent + protein); correct me if I'm wrong on this.  For
> very small molecules with 1,2 and 1,3 exclusions, this is zero.  For
> rigid molecules, its a trivial analytic calculation.
>
> For desolvation of molecules with internal degrees of freedom, it's
> more difficult, and we can't gloss over this step.
>
> Best,
> Michael
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