Using the novel thermodynamic extrapolation technique in molecular dynamics simulations, we investigate the interaction between phospholipid bilayers subject to various boundary conditions that correspond to established experimental methods for the determination of pressure–distance curves: the osmotic stress method, the hydrostatic method, and the surface force apparatus method. We discuss the roles of van der Waals and Helfrich undulation pressures in the force balance and find that they do not play a major role in the distance range below 28 water molecules per lipid as considered by us. We address the influence of experimental boundary conditions on bilayer structural changes as well as the consequences on interaction pressures. Significant discrepancies are observed between pressures obtained in osmotic stress and hydration methods on one hand and the surface force apparatus method on the other hand. We quantify the contribution of lipid volume compressibility to the total work of dehydration and find it to be substantial for high pressures. In a wide hydration range, the interaction pressure is mostly determined by the area per lipid molecule. This means that the influence of fatty acid chemistry on experimental pressure–distance curves is indirect and mediated by the area per lipid.