For protein structures relevant for autoimmunity, we performed simulations on 23 immune complexes and 4 antigen structures, obtaining single or multiple 100/200 ns trajectories, for each degree point between 37°C to 40°C. All files include PDBs obtained every 50 ns, starting with the initial structures at 0 ns. The datasets contain the full set of output files from Gromacs and processed data (RMSD, RMSF, Rg, SASA, H-bonds).  Binding free energies are available for some immune complexes.