[gmx-users] Re: Walls In Gromacs

Amit Choubey kgp.amit at gmail.com
Tue Nov 10 20:22:58 CET 2009

On Tue, Nov 10, 2009 at 4:32 AM, Marcovitz Amir <amarcovitz at gmail.com>wrote:

> Hi Amit,
> Unfortunately, i don't have an answer to your question as i am a very
> new GROMACS user myself..
> Actually i might need your help.

> I need to model two charged plates with opposite signs which are
> solvated in an electrolyte solution.

You might try to start with a boundary condition on the potential say
something like constant potential on the plates. And then you can always
find the electrostatic Green's function that solves the poisson's equation.
>From there you could derive an expression for the potential in the box if
the charge density were provided. This part is discussed in Classic
Electrodynamics book by Jackson. Have a look at it if you need reference.

You can use the above green's function for finding potential everywhere in
box depending on the location of ions in the solution. The force due to this
can then be implemented in MD. I am not very sure about the implementation

> When I was desperately browsing for
> keywords such as: Gromacs plates, walls, etc., trying to find the
> slightest clue of how to approach this issue in gromacs i saw your
> posting from the October 19th.
> I will most appreciate if you can give me some hint or tip of how to
> approach this problem or what is the suitable chapter in the manual to
> search for it.

I am not sure about any discussion on the specific type of things you are
talking about. Wall function for MD simulation is disscussed in chapter 7.
You will only find what options can be used. I think a tabulated function
can also be used.

> Sorry i couldn't help you with your question, hopefully you already
> figured it out,

I think it beneficial for both of us to keep these discussion in the forum
for our and other's benefit .


> Regards,
> Amir Marcovitz,
> Weizmann Inst. of Science , Rehovot, Israel
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