AMBER Archive (2002)

Subject: Re: how to neutralise the system?

From: David Case (case_at_scripps.edu)
Date: Mon Jan 14 2002 - 13:35:00 CST

On Mon, Jan 14, 2002, X. Tan wrote:

>
> I'd like to do some free energy perturbation work on a
> pentamer with two ligands. One is neutral, and the other with one unit
> negative charge. Since the pentamer has ten unit positive charges,
> associating with five same ligands. If I add ten positive charges for the
> first ligands' complex, then the other one still has five negative
> charges. So my question is how to neutralise the whole system? I wonder
> whether there is anyone having the similar experience. Any suggestions are
> welcome. Thanks a lot!
>

Clearly, if you are doing a perturbation between states of different total
charge, there is no way to have the system be neutral for both Hamiltonians.
With PME, gibbs should give reliable charging free energies anyway....see

%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

for a discussion of some of the factors involved in such calculations.

...good luck....dac 

-- 

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