This data set contains molecular dynamics (MD) simulation trajectories of human ribonucleases 1-7 and bovine ribonuclease A, in complex with two model nucleotide substrates ACAC and AUAU.The simulations where performed at two temperatures 300 K and 310 K, and in duplicates (two trajectories). The duration of the trajectories is 500 nanoseconds (ns). Larger files have been split in two parts.***Forthcoming publication: The paper related to this data set will be published soon.