Now that the system is assembled, create the binary input using grompp using this input parameter file:

gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr

Make sure you have been updating your topol.top file when running genbox and genion, or else you will get lots of nasty error messages ("number of coordinates in coordinate file does not match topology," etc).

We are now ready to invoke mdrun to carry out the EM:

gmx mdrun -v -deffnm em

For me, the system converged relatively quickly:

Steepest Descents converged to Fmax < 1000 in 143 steps
Potential Energy  = -4.9014547e+05
Maximum force     =  8.7411469e+02 on atom 27
Norm of force     =  5.6676244e+01

As in the lysozyme tutorial, it is possible to monitor various components of the potential energy using the energy module. I will not illustrate these principles here. Have fun.

Now that our system is at an energy minimum, we can begin real dynamics.