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This could be related to interplay between your model and Gazebo's (real-time) physics engine. Simulating dynamics is difficult and doing so in real-time requires a trade-off of speed vs. fidelity. It might be the case that your model indeed jitters at high frequency. I also often observed high noise in joint velocities (and thus, also accelerations) for complex robot models. You can decrease the physics engine step size and increase iterations from the Gazebo GUI. If things look better after you do so, the underlying simulation is indeed the cause. You then have the choice of either running simulation with these parameters (which will be slow), or trying to modify your model so there is less noise in simulation. The latter can be an art however and involves tweaking masses and inertias (and their relative magnitudes) while trying not to modify it too much.