[gmx-users] genion

[Tamas Horvath]

I have a protein in water system. The protein has some charge, which I want
to neutralise, introducing stochastic ammount of K+ or Cl-. As far as I
figured out, the best way to do it is to use genion. Only I don't know
beforehand what the protein's charge would be, so I'm wondering if it's
possible to tell genion to neutralise the system?

2nd.: If genion puts some ions in the system, are the ions considered as a
2nd protein?

Hota

On 12/21/05, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> Hi Tamas,
>
> You have to specify it yourself.
>
> Cheers,
>
> Tsjerk
>
> On 12/20/05, Tamas Horvath <hotafin at gmail.com> wrote:
> >
> > I want to neutralise my system (chargewise), so I use genion for that.
> > Do I always have to specify the number of ions to use, or is there a way
> > to automatically neutralise the system?
> >
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>
> --
>
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
>
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