Re: [AMBER] how to deal with the system with negative charge ?

From: case <>
Date: Tue, 30 Mar 2010 08:33:20 -0400

On Tue, Mar 30, 2010, sculiujl wrote:

> As usual we add ions to make the system neutralized. Now the system
> have seven negative charge, but I want to keep the system with one net
> negative charge .So how to dea with it in tleap? I wonder whether
> there is anyone having the similar experience. Any suggestions are
> welcome. Thanks a lot!

There is no problem with having a net charge, especially a small one, like
+/-1. We do simulations of ions all the time in developing force field

A "classic" paper on this is here:
%A T. Darden
%A D. Pearlman
%A L.G. Pedersen
%T Ionic charging free energies: Spherical versus periodic boundary
%J J. Chem. Phys.
%V 109
%P 10921-10935
%D 1998

...good luck...dac

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Received on Tue Mar 30 2010 - 06:00:03 PDT
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