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Abstract We present a computational study of sliding between gold clusters and a highly oriented pyrolytic graphite substrate, a material system that exhibits ultra-low friction due to structural lubricity. By means of molecular dynamics, it is found that clusters may undergo spontaneous rotations during manipulation as a result of elastic instability, leading to attenuated friction due to enhanced interfacial incommensurability. In the case of a free cluster, shear stresses exhibit a non-monotonic dependency on the strength of the tip-cluster interaction, whereby rigid clusters experience nearly constant shear stresses. Finally, it is shown that the suppression of the translational degrees of freedom of a cluster’s outermost-layer can partially annihilate out-of-plane phonon vibrations, which leads to a reduction of energy dissipation that is in compliance with Stokesian damping. It is projected that the physical insight attained by the study presented here will result in enhanced control and interpretation of manipulation experiments at structurally lubric contacts.