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

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 30 00:46:07 CEST 2010

Lum Nforbi wrote:
> 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.

I'm not 100% clear on your scenario.  If the Na+ ion is "part of the AOT 
molecule" then you shouldn't have to add anything, right?  There are two 
scenarios for including the parameters:

1. If the sodium ion is not part of the AOT [moleculetype] and coordinate file 
already, then you can add them with genion in the solvated system, and then just 
#include "ions.itp."  There is absolutely no difference between adding 100 Na+ 
ions to be considered part of the molecule (which is ionic, and probably 
dissociates in water anyway) and adding counterions.

2. If the Na+ ion is defined as part of the AOT [moleculetype] definition, then 
the atom type will already be defined within the force field parameter files and 
there is no need to #include "ions.itp" since the Na+ parameters will be 
explicitly included.

The choice is up to you, based on how the topology is organized.

> (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).

Two options:

1. Change your Gromacs mail preferences to not receive the list in digest form, 
instead you will receive individual messages.
2. Cut out the irrelevant text from the digest; there should still be some way 
to actually set a subject line.  Plenty of users on this list use Gmail, perhaps 
someone else can give better advice.


> 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
>  >


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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