Based on the loadings graphs, the different force fields are not sampling similar conformational space. The Amber ff14SB+OL3 and ff19SB+OL3 force fields have the highest weights around the residues 265 and 510, and the 5' end of the RNA (Figure , right panel and Supporting Information Table ). The loop of the RNA hairpin is located close to the flexible oligonucleotide binding domain (OBD) protein region around residue 265 and the movement of these interacting parts are connected. The first three nt of the 5' end of the RNA are moving rather freely and not interacting with the protein which might explain their higher effect on the first PC in these force fields. Residue 510 is part of a long loop (508-537) which forms part of the second recognition domain (RecII) which can interact with the 3' end of the RNA. This RecII domain is also visible on the loadings plots of the polarizable force fields. The highest loadings in the OPLS4 force field are observed around the middle region of the RNA and around residue 100 which forms a loop in the first recognition domain (RecI).