How to construst unit cell of water with hydrogen ions.

We are trying to build a simulation of a pore of Proton Exchange Membrane(used in Fuel cells) to calculate Proton(hydrogen ion) flux through it.
I would like to know that how can we build a amorphous cell consisting of water molecules with some hydrogen ions.
we tried to build a amorphous cell using hydrogen ions alone, but it resulted in failing of the Job.

Thank You