Prior to MD production runs, structures were first minimized then allowed to heat up from 0 K to 300 K for 40 ps. Production runs were performed in the NPT ensemble at 300 K. After heating, 50 ns production runs were performed in the NPT ensemble at 1 atm and 300 K. We used the Langevin thermostat with a collision frequency of 1 ps -1 and the Berendsen barostat with a relaxation time of 2 ps. Three separate 20 ns simulations were run with randomized starting trajectories and a time step of 1 fs for a total simulation time of 60 ns. After a buffer time of 5 ns, 300 configurational snapshots were uniformly sampled from each 60 ns trajectory, and fundamental base pair training units were obtained from these snapshots by stripping away all atoms apart from the central two base pairs and the waters required to sample the DNA-solvent interaction. Additionally, we obtain sample structures with Mg 2+ interacting with the phosphate group by including configurations where the Mg-O atomic distance was less than 2 Å. In addition to this DNA-solvent training set, ionic solvation shells were sampled by extracting water shells around ions outside the influence of the DNA.