Antimicrobial peptides (AMPs), which are found among all classes of life, are able to kill bacteria, enveloped virus, and fungi. Unlike the conventional antibiotics, AMPs kill bacteria by permeabilizing their membranes. Though there have been many different antimicrobial mechanisms based on assumptions of microscopic peptide-membrane structures, very few of these structures have direct experimental evidence. Meanwhile, molecular dynamics simulation of AMPs is also constrained by the charges on most AMPs. In this talk, I will first show our recent study on transmembrane permeation of charged groups based on free energy calculation. A water-bridge mechanism is shown to be able to significantly reduce the free energy barrier of the transmembrane permeation of ions. Then I will present a 0.2 millisecond unbiased all-atom simulation on a specific AMP. In this simulation, we observe that the water-bridge mechanism is a main mechanism for the translocation of charged and highly polarized groups. Our simulation clearly demonstrates that a class of AMPs can form dynamic transmembrane oligomers, which can lead to leakage of ions (Na+ and CL-) and translocation of lipid molecules. Our long time simulation also allows us to study the statistical properties of the oligomers and their functions.