David Mobley wrote:
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.
I can't comment on the effectiveness of PME on such a system with FEP/TI.
Mark
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