On Wed, Dec 07, 2011, Surya Prakash Tiwari wrote:
>
> I was wondering whether *charged system correction
> term*(-(1/(8*epsilon_0*kappa^2*L^3))*(Sum over q^2)) has been
> implemented in the
> PME implementation of AMBER.
>
> I am talking about the last term of eqn. 15 on page 8 of the following
> paper:
>
> Warren, G. L., & Patel, S. (2007). Hydration free energies of monovalent
> ions in transferable intermolecular potential four point fluctuating charge
> water: an assessment of simulation methodology and force field performance
> and transferability. The Journal of chemical physics, 127(6), 064509.
> doi:10.1063/1.2771550
No. (You might double-check with Tom Darden). The "amber" approach to
these finite size corrections is to extrapolate "uncorrected" simultions
as a function of system size, as outlined here:
%A T. Darden
%A D. Pearlman
%A L.G. Pedersen
%T Ionic charging free energies: Spherical versus periodic boundary
conditions
%J J. Chem. Phys.
%V 109
%P 10921-10935
%D 1998
(See esp. Eq. 2.24 and Tables III and IV). The procedure that Warren and
Patel apply shows excellent conversion to the final result (e.g. their Fig.
2).
...dac
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Received on Thu Dec 08 2011 - 06:00:02 PST
