From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sat Nov 22 2008 - 16:30:52 CST
> I'd like to estimate the free energy difference for
> prot(Arg)+env.=>prot(Ala)+env. (II)
That was my question, actually. Is it the free energy of solvation, or
interaction with the environment that you are interested in? If not,
what is it, i.e. how do you define it?
Also, the point of mutating a counterion is to do it in the same
simulation as the charged residue is mutated. It is a way to keep the
effective total charge of the system neutral at all times. Simulations
of charged systems in periodic boundary conditions with long-range
electrostatics (e.g. PME) may carry a risk of artefacts - people
usually stay on the safe side by keeping their systems neutral.
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