Atomistic molecular dynamics simulations were used to study the interaction of AnK peptides (with n = 3, 6 and 9) in contact with two different types of lipid membranes, DPPC and DPPG. PMF calculations and their decomposition into enthalpic and entropic components allowed a detailed thermodynamic analysis of the energy profile associated with the adsorption and penetration of the peptides through the lipid membranes. Our simulations indicated a drastic difference between the interactions of the peptides with both membranes. For the peptide A6K the interaction with the DPPG and DPPC membranes were −222 kJ mol−1 and −16 kJ mol−1, respectively. PMF for the DPPC membrane did not show any minimum in the interface region, that is, no favorable interaction with its surface. On the other hand, the interaction with the DPPG membrane showed a clear minimum near the surface. This minimum, although shallow, −10 kJ mol−1, indicates that the adhesion of the AnK peptides on the surface of the DPPG membranes is a favorable process.