[gmx-users] Re: How to include sodium ion (Reply to Justin's mail)

[Lum Nforbi]

Justin,

    The sodium ion I am talking about is part of the docusate sodium salt
(AOT). If I want to solvate 100 AOT molecules with water molecules, how do I
make sodium ions part of the system? I am not just adding sodium ions to
balance the charge of the system. The sodium ions are part of the AOT
molecules, so I need 100 sodium ions in the system. Do I just add one sodium
ion in the parameter file containing the rest of the 65 atoms of AOT, then
specify #include "ions.itp" in the fopology?
I appreciate your answers.

(Aside: Can you help with replying emails via this forum. I use gmail and
when I click the reply tab, it includes all the mails for that issue, and
there is no "subject" entry. So I always have to copy and paste the mail
before replying. I appreciate your help).


Lum Nforbi wrote:
> Hi All,
>
>    I would like to include sodium ions into a water/AOT (sodium
> di-2-ethylhexylsulfoccinate) cubic box. Can someone tell me how to do
> this and how to include parameters for the sodium ion in the parameter
file?
> I appreciate your answers.

Shouldn't this be as simple as using genion and then:

#include "ions.itp"

in the topology?  Or is there some other problem you're having?

-Justin

>
> Lum
>
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