Trajectories generated with WaterKit can therefore be used to replace MD simulations, presenting a number of advantages. It requires minimal user input, such as the target structure and the location and size of the region to analyze, which unlike MD simulations, can include only a subset of the protein volume. WaterKit seems to be less sensitive than MD simulations to the initial conformation of the target. While target atoms are constrained with both methods, the iterative placement and the ensemble sampling used in WaterKit appears to make it less sensitive to the initial conformation (see HIV-1 protease case study). Also, due to the method in which water positions is sampled, WaterKit is intrinsically less sensitive to aberrations resulting from trapped water molecules, i.e.: water molecules confined in buried cavities that have difficulty equilibrating between the binding site and the bulk solvent. To address this issue with MD simulations, dedicated approaches have been devised to facilitate this exchange , but there are a number of resulting challenges, from the varying number of water molecules during the simulation, to computational inefficiencies. Equilibration issues might be source of some of the discrepancies we reported in some of the systems (neuraminidase, HIV-1 protease and FABP4). This is a first step in the direction of integrating more sophisticated solvation model methods in the AutoDock protocol. The Python prototypical implementation presented here showed execution times that are competitive with highly optimized GPU-accelerated MD code. On average, a WaterKit calculation takes less than 2 hours to generate an ensemble of 10.000 frames on Intel Xeon E5-2640 v3 @ 2.60GHz (32 cores). We anticipate that when porting the protocol from Python to optimized GPU code, we can achieve speed increments from 100x to 1000x times, hinting at execution times very well under a minute. This would allow the inclusion of this protocol as a step of the docking process, providing a rapid way to recalculate multiple water molecule network arrangements resulting from ligand binding.