Nanoporous materials are of interest in many applications due to their high surface area and physicochemical properties, including a high pore volume and good thermal and mechanical stabilities. The interconnected channels can be used for “flow-through” applications such as purification of drinking water or nanoseparation of proteins or organic solvents. The objectives of this work are to evaluate the impact of (i) nanomaterial kind, (ii) pore size, (iii) pore shape, and (iv) solvent polarity on the material's permeability in comparison to experimental data. Using coarse-grained molecular dynamics (MD) we will establish molecular models of 3D structures of amorph carbonaceous materials and of diverse metal-organic frameworks. Thereby, the force field parameters will be determined from atomistic MD simulations and based on experimental data. Both, these parameters and the home-written material building tools will be shared with the scientific community. Next, variation of the pore diameter, surface functionalization and solvent polarity enables us to systematically evaluate the impact of the individual material properties on e.g. molecular transport, solvent competition, and nanoseparation.