Why Do I Get Different Results Each Time From AutoDock Vina?
Vina uses a non-deterministic docking algorithm. See the manual.

The docking algorithm is non-deterministic. Even though with this receptor-ligand pair, the minimum of the scoring function corresponds to the correct conformation, the docking algorithm sometimes fails to find it. Try several times and see for yourself. Note that the probability of failing to find the mininum may be different with a different system.

The manual states that you can set the random seed in order to obtain reproducibility.

I changed something, and now the docking results are different. Why?
Firstly, had you not changed anything, some results could have been different anyway, due to the non-deterministic nature of the search algorithm. Exact reproducibility can be assured by supplying the same random seed to both calculations, but only if all other inputs and parameters are the same as well. Even minor changes to the input can have an effect similar to a new random seed. What does make sense discussing are the statistical properties of the calculations: e.g. &quot;with the new protonation state, Vina is much less likely to find the correct docked conformation&quot;.