​We present results of simulations based on a physics-based depositional model of sandstone. The initial rock sediment is modeled as a pack of spherical grains. The absolute permeability is estimated directly from the digitized images of computer-generated rock using lattice-Boltzmann flow simulations. The local connectivity of the pore space is analyzed using the local porosity theory. In the simulated scenarios, the porosity and permeability are reduced by compaction and cementation. The computed porosity–permeability relationships match well the laboratory measurements, and are similar to the power-law of Kozeny–Carman equation. It turns out that the exponent depends on the grain size distribution and cementation pattern. Therefore, it is not universal. The approach and results are also applicable for predicting permeability modification caused by mineral precipitation and chemical reactions in transport problems.