AMBER Archive (2008)

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

From: Markus Kaukonen (
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

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=  \ 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+ ______
--- Rikos ei kannata, eika maatalous Suomessa. (Paimio 1998) ---

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to