This dataset relates to 2 ns molecular dynamics simulations of water in zeolite HY at loadings of 5–33 wt%, in systems with Si/Al ratios ranging from 5 to fully siliceous. Included are the input and output files of the simulations, carried out using DLPLOY 4, needed to reproduce all data and analysis in the publication "A classical molecular dynamics study into the effect of Si/Al ratio and silanol nest defects on water diffusion in zeolite HY".