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Three-dimensional correlations of the Lyman-$α$ (Ly$α$) forest and cross correlations between the Ly$α$ forest and quasars have been measured on large scales, allowing a precise measurement of the baryon acoustic oscillation (BAO) feature at redshifts $z>2$. These 3D correlations are often modelled using linear perturbation theory, but full-shape analyses to extract cosmological information beyond BAO will require more realistic models capable of describing non-linearities present at smaller scales. We present a measurement of the Ly$α$ forest flux power spectrum from large hydrodynamic simulations -- the Sherwood simulations -- and compare it to different models describing the small-scale deviations from linear theory. We confirm that the model presented in Arinyo-i-Prats et al. (2015) fits the measured 3D power up to $k=10\, h\rm{Mpc^{-1}}$ with an accuracy better than 5%, and show that the same model can also describe the 1D correlations with similar precision. We also present, for the first time, an equivalent study for the cross-power spectrum of halos with the Ly$α$ forest, and we discuss different challenges we face when modelling the cross-power spectrum beyond linear scales. We make all our measured power spectra public in \url{https://github.com/andreufont/sherwood_p3d}. This study is a step towards joint analyses of 1D and 3D flux correlations, and towards using the quasar-Ly$α$ cross-correlation beyond BAO analyses.