From: Rajan Vatassery (rajan_at_umn.edu)
Date: Sat Jan 28 2012 - 15:31:18 CST
I had a similar concern regarding my simulations, and I found Peter
Freddolino and Axel Kohlmeyer's responses on this thread to be useful:
On Sat, 2012-01-28 at 14:35 -0500, Thomas Albers wrote:
> 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?
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