We employ atomistic molecular dynamics simulations to predict the alignment and anchoring strength of a typical nematic liquid crystal, 4-n-penty1-4'-cyano biphenyl (5CB), on different forms of silica. In particular, we study a thin (similar to 20 nm) film of 5CB supported on surfaces of crystalline (cristobalite) and amorphous silica of different roughness. We find that the orientational order at the surface and the anchoring strength depend on the morphology of the silica surface and its roughness. Cristobalite yields a uniform planar orientation and increases the order at the surface with respect to the bulk whereas amorphous glass has a disordering effect. Despite the low order at the amorphous surfaces, a planar orientation is established with a persistence length into the film higher than the one obtained for cristobalite.