We investigate membrane permeation by the peptide WKW that is amidated at its C-terminus and therefore carries a positive charge of +2. To facilitate an efficient calculation, we introduce a novel set of simple coarse variables that measure permeation depth and membrane distortion. The phospholipid head groups shift toward the center of the membrane, following the permeating peptide, and create a defect that assists permeation. The Milestoning algorithm was used in the new coarse space to compute the free energy profile and the mean first passage time. The barrier was lower than expected from a simple continuum estimate. This behavior is consistent with the known behavior of positively-charged cell penetrating peptides, and is explained by a detailed mechanism of defect formation and propagation revealed by the simulations.