Alchemical free-energy methods and electroneutrality

From: Thomas Albers (talbers_at_binghamton.edu)
Date: Sat Jan 28 2012 - 13:35:27 CST

Hello!

I seem to remember that systems simulated with periodic boundary
conditions must be electroneutral, or systematic errors will be
introduced through PME method.

There's the Alchemical Free-Energy tutorial, where one of the examples
is the potassium ion-18-crown-6 complex. In the tutorial, the
potassium ion is made to vanish, but not its countercation. Does the
error introduced through non-electroneutrality cancel itself out
through the thermodynamic cycle, or should for the correct treatment
the counter-anion also be made to vanish?

Thomas

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