The main structural element of biological membranes is a liquid-crystalline lipid bilayer. Other constituents i.e. proteins, sterols and carbohydrates, either intercalate into or loosely attach to the bilayer. Many properties common to the membranes can be explored by studying lipid bilayers. In this paper, the molecular dynamics simulation method was applied to study membranes at various levels of compositional complexity. Whenever it was possible, results of the simulations were compared with published experimental data. The reactive site loop of a1-antitrypsin is held in a tightly constrained conformation by a salt bridge between Glu342 and Lys290. Guanidinium ions induce a1-antitrypsin polymerisation by disrupting this salt bridge. The mechanism of this process, proposed on the basis of experimental studies, was confirmed and further explained by molecular modelling methods.