'Structures' folder contains: PDB files with representative structures of top clusters (those with occupancy >5%) found for each system. Clustering was done using RMSD as a similarity measure between the structures in simulated trajectories. 'Setup_files' folder contains: (1) Topology files (*top), input structures for the simulations (*qtop_oplsaa.pdb) and files containing additional parameters and settings used in the simulations (*fep) for each simulated system. (2) Sample inputs for a single MD run (sample-md-inputs subfolder) including initialization, heating and pre-equilibration phase (0-dyn*inp to 8-dyn*inp and dyn_eq300k.inp), and a sample input for the subsequent equilibration/production phase (dyn_15ns.inp). Production phase was carried out until the lenght of the simulation specified in the methodology section was reached. Multiple trajectories simulated for each system were generated by carrying out the simulation in five independent replicas, with each one initialized with a different random seed specified in 0-dyn*inp file. The sample inputs are taken from a NDM1-WT simulation run.