Using the molecular dynamics method, the mechanisms of action and characteristic properties of three types of antimicrobial peptides (AMPs) (adepanin-1, diPGLa-H and six of its analogues kiadins and anisaxin-2S) were investigated in interaction with plasma membrane models of Gram-positive, inner and outer membranes of Gram-negative bacteria, and neutral membranes of eukaryotes. Atomistic, united atom and coarse-grained simulations were performed. The simulations investigate the importance of peptide structuring, their flexibility, clustering and other properties important for antimicrobial activity. It is shown how peptide associations can help to place peptides in a position and conformation favorable for their insertion into the membrane. Analysis of how the number and position of the amino acid glycine changes the properties of the peptide and affects its interaction with the membrane showed that the position is more important than the number of glycine in the peptide sequence. It has been confirmed that the mechanism of action of AMP can include the complete extraction of lipids from the upper membrane layer achieved with high local concentrations of peptides on the membrane surface. It is possible that this type of lipid extraction is the first step in the mechanism of action, and that the resulting asymmetry in the local density of lipids in the two membrane layers can reduce the energy barrier for peptide insertion. This thesis contributes to a better understanding of the mechanism of action and the antibiotic potential of antimicrobial peptides.