Lattice-Boltzmann (LB) simulations are a common tool to numerically estimate the permeability of porous media. For valuable results, the porous structure has to be well resolved resulting in a large computational effort as well as high memory demands. In order to estimate the permeability of realistic samples, it is of importance to not only implement very efficient codes, but also to choose the most appropriate simulation setup to achieve accurate results. With the focus on accuracy and computational effort, we present a comparison between different methods to apply an effective pressure gradient, efficient boundary conditions, as well as two LB implementations based on pore-matrix and pore-list data structures.