Surface effects become important in microfluidic setups because the surface to volume ratio becomes large. In such setups the surface roughness is not any longer small compared to the length scale of the system and the wetting properties of the wall have an important influence on the flow. However, the knowledge about the interplay of surface roughness and hydrophobic fluid-surface interaction is still very limited because these properties cannot be decoupled easily in experiments. We investigate the problem by means of lattice Boltzmann (LB) simulations of rough microchannels with a tunable fluid-wall interaction. We introduce an ``effective no-slip plane at an intermediate position between peaks and valleys of the surface and observe how the position of the wall may change due to surface roughness and hydrophobic interactions. We find that the position of the effective wall, in the case of a Gaussian distributed roughness depends linearly on the width of the distribution. Further we are able to show that roughness creates a non-linear effect on the slip length for hydrophobic boundaries.
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