In one aspect of the invention, each bolt is modeled using a beam element in a FEA model. To apply desired pretension to one or more bolts, at least one pretension-versus-time curve is specified. Each pretension-versus-time curve includes ramp portion, desired pretension portion and optional unloading portion. Ramp portion starts from zero to desired pretension in a substantially linear manner, and hence being configured for applying desired pretension to a bolt gradually with smaller increments. Desired pretension portion is configured for ensuring the desired pretension can actually be applied to the beam element during an initialization process - a series of quasi-static analyses. Since the method is independent of the deformation of the beam, the method completely avoids the need to iteratively determine an axial strain or displacement that gives the desired pretension.