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
--
-----------www= http://www.iki.fi/markus.kaukonen---------------
Markus.Kaukonen.teokem.lu.se \ HOME-> Viinirinne 3 F 12
Dep. of Theoretical Chemistry \_______ 02630 Espoo, Finland
Lund University \ tel:+358-(0)9-5127122/h
Chemical Centre, P. O. Box 124 \____+358-(0)45-1242068/mob
S-221 00, Lund, Sweden \______ H+ ______
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Received on Sun Jun 01 2008 - 06:07:04 PDT
