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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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