The Cas12j system has overall higher RMSD values than the Ago2 system. The protein is not as compact and globular as Ago2 and there is more freedom of movement also for the RNA. The higher RMSD values do not necessarily mean that the system is fluctuating more, as they could be a result of the initial structure being further away from a local energy minimum. Then, in the simulations the system adopts an energetically more favorable conformation which is by RMSD further away from the initial one and fluctuates around that conformation. As the deviations of the RMSD values are like those of Ago2, this seems to be the case with Cas12j. The Amber force fields display the least fluctuating protein and RNA, and the largest RMSD values are observed in the AMOEBA and O3P systems for the protein and in the OPLS4 and O3P systems for the RNA. The Zn ion stays in place in ff14SB+OL3 and AMOEBA force fields, in the other ones it unbinds. This leads to overall structural instability which is most obvious in the O3P simulations (Figure ).