The energy minimization and equilibration steps are going to be conducted just like any other protein-in-water system. Here, we will perform steepest descents minimization followed by NPT equilibration. The .mdp file for minimization can be found here, and the one for NPT equilibration can be found here.

Invoke grompp and mdrun, as usual:

gmx grompp -f minim.mdp -c solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

gmx grompp -f npt.mdp -c em.gro -p topol.top -r em.gro -o npt.tpr
gmx mdrun -deffnm npt