[gmx-users] Free energy for charged molecules

David Mobley dmobley at gmail.com
Fri Sep 22 14:55:30 CEST 2006


> Thanks for your reply. I had actually search the archives but didn't
> find any clear answer (maybe the search was not so good)... You mention
> this is a problem with PME, would plain Ewald or even Reaction-Field be
> less problematic in this case? And how large do you estimate the cutoff
> should be to give reasonable results? My system is a small molecule
> (~20 atoms) in water, so I can afford building boxes with a lot of
> solvent.

Sorry, instead of PME, I should have said "lattice sum
electrostatics", which all have the same requirement that the system
be net neutral. Things are different with reaction field, but it is
still not clear that one gets the "right answer".

There is a recent paper which has been mentioned on the list by
Hunenberger, I believe, which computes the hydration free energy of a
sodium ion with several different methods including lattice-sum and
reaction field and gets the same answer by applying appropriate
corrections. But so far I haven't been able to understand it. You
might want to look that one up. Again, don't just assume that if you
use the right treatment of electrostatics it will just "work" in the
sense of giving you the right answer: Things seem to be far more
complicated than that.


> Thanks,
> Ignacio Fernández Galván
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