[gmx-users] FEP

David Mobley dmobley at gmail.com
Thu Mar 23 22:22:47 CET 2006


> I am rather nervous about doing FEP/TI for disappearing charged
> > molecules, as it is not at all clear to me that it is possible do this
> > correctly with current methods. Perhaps someone else may be able to
> > comment more, but at least with long range electrostatics (PME), systems
> > are required to be neutral. It IS possible to apply PME to a "charged"
> > system, but I think this is typically done by spreading a uniform
> > neutralizing charge throughout the box. It isn't clear that this is
> > really correct for FEP/TI, I don't think, since in that case you will
> > have a charged molecule overlapping with some of the uniform
> > neutralizing charge, which could give strange energy artifacts.
> In general, PME can be applied to a system with any charge. The PME
> section of the gromacs manual is silent on this topic, and I've never
> tried to do it, however. You are correct about the uniform neutralizing
> charge throughout the box, but this is present for *every* partial
> charge in the system, each of which contributes individually in the
> Ewald summations. The utility of that as a physical model is a different
> question, however.

Thanks for the comments. Just to clarify what I meant about energy
artifacts, if you are compute the free energy of turning off a charge which
overlaps with a uniform neutralizing charge, suddenly the density of that
uniform neutralizing charge becomes quite important (at least, it seems like
it would) since the free energy of turning off the charge depends on the
surrounding charges... That's the part that seems concerning. (More so for
when the neutralizing charge overlap with a given atom is constant, as in
PME when FEP/TI is NOT done -- in which case it seems clear it doesn't
contribute to the dynamics or free energies in any way).


I can't comment on the effectiveness of PME on such a system with FEP/TI.
> Mark
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