[gmx-developers] Reaction field questions (David van der Spoel)

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Wed Mar 4 20:23:22 CET 2015

>I wouldn't agree with this. The Hamiltonian is well defined and you do
>sample a Boltzmann distribution. But the Hamiltonian and distribution
>might be very different from the "correct" Hamiltonian. GB and RF are
>effective free-energies, as averaged over certain conditions. If the
>conditions you use them in are different from the conditions used to
>derive the potential (free-energy), than your results might differ (be
>wrong) a bit or a lot.

I'll agree with Berk as well.  I think the key is if you are averaging out
components, then you have lost some entropy, in which case the temperature
dependence will necessarily become nonequivalent to the original
temperature dependence.

In systems w/o long range order (gases, fluids w/o interfaces, or
proteins) then very little entropy is being is being lost.  When there is
long range order (interfaces, crystals), you are losing something by going
to anything approach that uses averages.

Note that Ewald also loses something by averaging over unit cells, but
it's not as much as by averaging outside a 1 nm or so cutoff.

Michael Shirts
Associate Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434) 243-1821

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