Cell-penetrating peptides can permeate through the plasma membrane. The permeation ability is useful for delivery of bioactive molecules. Experiments suggest that the binding between the guanidino group in the peptide and lipid headgroups is of crucial importance in the peptide permeation through lipid membranes. We investigate the free energy profile for the permeation of the peptide through the lipid bilayer membrane with changing the binding strength by a series of coarse-grained molecular dynamics simulation. We found that the energy barrier for the permeation has the minimum at the medium strength of the binding (∼2ε). Our result suggests that the appropriate attractive interaction between peptide and lipid headgroups enhances the permeation of the peptide across the lipid membranes.