AMBER Archive (2008)

Subject: AMBER: Hydration free energies of charged ions using PME

From: Markus Kaukonen (mka_at_fyslab.hut.fi)
Date: Wed May 28 2008 - 01:51:26 CDT

Dear All,

I was reading an article by Warren&Patel (J. Chem. Phys v127 064509
y2007), where absolute hydration free energies of monovalent ions were
calculated.

Question: For periodic charged systems there are plenty of
corrections, I got confused when reading the amber manual&mailing
lists&references on what of these corrections are included and what not.

In particular, are the surface-dipole (~1/L^3 *Sum(q_i*r_i)^2 ) and
charged system correction term (~-(1/L^3)*Sum(q_i)^2 in the total
energy of amber (Eq. 5 last two terms in the paper by Warren)?
Furthermore, is the Wigner potential of an ion taken into account in
some way (~q/L) ? (L is the length of a side of the simulation cube, q_i
is the charge of an ion, q is the total charge of the system) ?

Finally, could somebody point out a publication were
standard-periodic-AMBER would have been used to calculate absolute
free energies for charged systems?

Terveisin, Markus 

-- 
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