Human β defensin type 3 (hBD-3) is a cationic (+11 charged) antimicrobial peptide. It has three pairs of intramolecular disulfide bonds which can break under reducing conditions to convert hBD-3 into the linear analog form. hBD-3 can disrupt both Gram-positive and Gram-negative cell membranes, and even the mammalian cell membrane at high concentrations. However, the structural basis for the membrane-disrupting function of hBD-3 is still unknown. In order to understand the interaction mechanism of hBD-3 with a neutrally charged lipid membrane, explicit solvent and lipid umbrella-sampling simulations were performed using the NAMD program on the hBD-3 wild-type and the linear analog, in both the monomer and dimer forms. During the insertion and translocation process, most of the protein structure changes take place near the membrane-solvent interface, while the membrane interior appears to stabilize and rigidify the native-like hBD-3 structure. An energy barrier of 20 kcal/mol (domain unit) should be overcome by hBD-3 dimer in wild-type to cross the POPC bilayer but only 13 kcal/mol (domain unit) to insert into the bilayer center, and 20 kcal/mol for hBD-3 monomers to insert into the membrane center. Significant reorientation of lipids around hBD-3 inside the membranes was observed, which suggests a toroidal model for the membrane disruption process.