This step is conducted much like any other simulation. Refer to the Lysozyme tutorial for a more detailed description of what is going on here if you are unsure. First, we will add water with solvate:

gmx solvate -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top

Next, we will add ions using genion, utilizing this .mdp file. We are going to be conducting these simulations in the presence of 100 mM NaCl, on top of neutralizing counterions:

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1

Select group 13 (SOL) to replace water molecules with ions.