[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:
> 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
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).
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?
> > Lum
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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