creating ions

[sathyajit]

Hi,

How do I create ions (ex. Na+, Cl-) to simulate the ion dissociation in water  and its effect on a bulk configuration ?

I know how to get the element Na or Cl, but I am not sure about getting the individual ions in place.

Thanks
Sathyajit

[zh]

You may put  one (n) Na  atom(s) and one (n) Cl atoms in a box with proper number (determined by the density of liquid water and the simulation box) of water molecules and then do the NVT molecular dynamics simulations. After sufficient MD steps, the simulation may reach the thermodynamic equilibrium state of the dissociated Na+ and Cl- ions in water.  Note that in such setup, the whole simulation is neutral.  You also can check the charge states of Na and Cl atoms in the equilibrium state by the Mulliken charge population analysis. The charge states of Na and Cl atoms may be nearly close to +1 and -1 ,respectively.

[reallusion]

Then how to deal with the situation where the ions is in acid or alkaline solutions with different pH value. Thank you.

[Jess Wellendorff]

For acidic or alkaline solutions, I guess you will need to explicitly consider some suitable concentration of H+ and OH- ions.