In the Amber simulations, the protein is fluctuating more than either of the RNA strands. In the OPLS4 and AMOEBA force fields, the situation is the opposite, and the RNA fluctuates more than the protein. The fluctuations of the guide RNA are more pronounced in the polarizable force fields and around nucleotides 9-18 which are not tightly bound to the protein. Some of the RNA stabilization in OPLS4 force field is caused by an extra hydrogen bond forming between the guide RNA U1 and the target RNA A2 (Figure ). For the protein, the longer loop regions around residues 110, 605 and 830 appear to fluctuate more in the Amber ff19SB+OL3 force field and the O3P water systems, but otherwise the trends in the RMSF graph are similar in all the tested force fields (Figure and Supporting Information Figure ). The longer loops around residues 110 and 830 are very much fluctuating in the O3P simulations but this does not lead to overall structural instability in these 500 ns simulations. The Mg ion in the AGO2 system is tightly bound between the protein and the RNA and it remains in its position in all simulations in all force fields.