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From: Basak Isin (isinbasak_at_yahoo.com)
Date: Thu Jul 18 2013 - 13:16:18 CDT

Sent from my iPhone

On Jul 18, 2013, at 11:10 AM, Adrian <adpala_at_hotmail.com> wrote:

> Hi,
>
> I'm interested in running some simulations using implicit water (as in the namd tutorial 1-4, for example), but I notice you are not supposed to explicitly ionize your system in such cases, but I do need to consider explicitly the ions, as that's my main interest.
>
> If I add the ions to the the pdb and delete water molecules, would it be correct to continue the procedure for GBIS (generalized born implicit solvent)?
>
> If not, what would be the correct approach?
>
>
>
>
>
> Thanks for your time!!
>
> Adrian Palacios
>

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