The data set 10.5281/zenodo.3688506 contains the raw data used for the preparation of the manuscript 'Sodium-induced population shift drives activation of thrombin' (doi:10.1038/s41598-020-57822-0). To limit the required storage space, the trajectories are deposited only as coordinates of the analysed loop. The data set is separated into following parts: X-ray: Data used in the analysis of the PDB structures of thrombin, including a list of the PDB IDs, results of the PCA and values of the introduced features in the structures. cMD: Input parameters, topologies and starting coordinates of classical MD simulation based on different PDB structures (3bei, 3lu9 – with Na+ ions and without Na+ ions), resulting trajectories, projection on X-ray PCA and values of the introduced features during the simulations. TMD: Input parameters, topologies and starting coordinates of the targeted MD simulations, resulting trajectories, projection on X-ray PCA and RMSD values. Seeded-Simulations: Input parameters, topologies and starting coordinates of classical MD simulations that are started from cluster representatives of the TMD simulations and resulting trajectories (3*100 simulations, each lasting 200 ns), separated into simulations with Na+ and without Na+, additionally values of the introduced features during the simulations. MSM: For both systems (with and without Na+), files are provided that can be loaded with pyemma (TICA objects, kmeans clusterings, calculated implied timescales and MSMs); additionally TICs of the seeded simulations, psi-dihedrals of the seeded simulations, RMSD values of the E and E* states and representative structures of the E and E* states A more detailed description of the included files can be found in the README files in each folder.