[gmx-users] question regarding genion

[Vigneshwar Ramakrishnan]

Hi Sarbani,

I think you should use "genion -random no" along with other options.

Thanks,
Vignesh

On Fri, Sep 12, 2008 at 3:30 PM, sarbani chattopadhyay <
sarbani_c84 at rediffmail.com> wrote:

>   Hi everybody,
>                       I want to place my counterions close to the charged
> amino acids. I am aware of
> the fact that even if the counterions are randomly added yet they will
> eventually settle during
> equlibration. But still I will like to start with a structure that has
> counterions close to charged
> residues.
> I have been going through the archive and the manual but I could not figure
> out how to
> disable the default option of "-random" while using the "genion" command.
>
> Can anyone guide me through the command that is required to add counterions
> based on
> potential so that the counterions are closed to the charged residues?
>
> Thanks  in advance
> Sarbani
>
>
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-- 
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

"The rewards of sincere resolves are highs money can never buy!"
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