AMBER Archive (2009)

Subject: [AMBER] Counterion release and Free energy of binding ?

From: Marek Maly (
Date: Tue Jul 14 2009 - 17:27:18 CDT

Hi all,

recently I read an interesting article from Zhaoyang Ou and M. Muthukumar:

"Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics

In this article authors discuss counterion release during complexation
process of two oppositely charged polyelectrolytes
with respect to free energy of binding.

The authors state that entropy gain of the whole system due to the release
of counterions which was originally adsorbed on stand alone
could be in some conditions more important than change in culombic energy
during the complexation. They speak here about "entropy driven

If I understood well it would be appropriate to take in account counterion
release for the calculation of free energy of binding
(i.e. enthalpy change caused by this effect but mainly the entropy gain).

I am really curious about the opinion of other Amber users and mainly of
the Amber developers
(for example if they plan to add this counterion contribution into free
energy of binding calculation in Amber).

In my opinion the effect of counterion release is significant only in
specific cases like
in article discussed case of highly charged and very flexible
polyelectrolytes which are able to create very tight
complexes and collaps together which is accompanied by massive release of
counterions, but It is just my private
opinion and I would appreciate some discussion on this topic. At least to
know the right comments when someone
asks me next time in conference plenum "Did you take in account counterion
release for free energy of binding calculation ? " :))

Thanks to all in advance for valuable comments.

Best regards,


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