Now that we have solvated our system and removed water molecules from the hydrophobic core of the membrane, it is time to add neutralizing counterions. At this point, the process for continuing with building our system is nearly identical to that of the lysozyme tutorial. The .mdp file used can be found here.

gmx grompp -f ions.mdp -c system_solv_fix.gro -p topol.top -o ions.tpr

Since the KALP₁₅ peptide contains 4 lysine residues, the peptide bears a net charge of +4e at neutral pH. Use genion to add 4 Cl^- ions to neutralize this charge:

gmx genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -neutral