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Hexane is the shortest representative of the family of alkanes (linear models for polymers and proteins having formula CH3-(CH2)n-2-CH3 whose flexibility has any considerable impact on its dynamics. When adsorbed on graphite, a monolayer of hexane melts from a herringbone solid to a liquid at a temperature of approximately 175 K. To understand the mechanisms that drive this transition we have performed large scale molecular dynamics simulations (several runs over 100 ns, requiring a total of ~10 cpu-years of computation), using the most realistic model of the system (a fully atomistic representation of hexane, explicit site-by-site interaction with graphite carbons and CHARMM force field with carefully chosen adjustable parameters of interactions). We show that the melting of the low temperature herringbone solid phase starts with the formation of gauche defects at the ends of neighboring molecules, followed by molecular reorientation within a lamellae, without perturbing the overall structure of the adsorbed film. The melted phase has a domain-type structure with domains’ orientation that reflects the 6–fold symmetry of graphite. The size of domains decreases progressively when the temperature increases and the deformation of molecules to quasi globular shape is driven by progressive formation of gauche defects. Work supported by the U.S. Department of Energy (DE-FG02-07ER46411) and the American Chemical Society Petroleum Research Fund (PRF43277-B5). Computational resources were provided by the University of Missouri Bioinformatics Consortium.