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We have studied the alignment and molecular organisation within a thin film of the popular nematic 5CB sandwiched between two flat polymer slabs, examining the effect of polymer chemical nature and morphology with atomistic molecular dynamics simulations. We have chosen two common polymers: polystyrene (PS) and polymethylmethacrylate (PMMA), either with their chains in random coil conformation (disordered) or with chains unidirectionally stretched (ordered). We found that, independently on the arrangement of the chains, both surfaces align planarly the liquid crystal, in accord with experimental observation. Moreover, while 5CB molecules align along the chains stretching direction of the PMMA ordered surface, on the combed PS surface they arrange on average perpendicularly to the stretching direction. This behaviour is attributed to the chemically specific interactions between the respective aromatic moieties of PS and 5CB. [ABSTRACT FROM AUTHOR]