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I am using the analyze tool to investigate body kinematics. The problem is that the linear acceleration values are clearly wrong. I have attached the velocity and acceleration graphs. As you can see, acceleration is near 50 m/s^2 while velocity is staying nearly level. I am simply opening the analyze tool, setting the motion from an IK file, and adding the body kinematics analysis. Any ideas on what I can be doing wrong here?

Yes it seems strange. My guess is that you are not applying any force in the analysis. In case that you are analyzing a gait you can try to add the ground reaction forces. In theory body kinematics shouldn't rely on the kinetics, but the internal implementation of the analyze tool, which is very generic, may requires them because the state is realized to acceleration. This means that the acceleration is calculated from the applied forces. I am not 100% sure, but you can try this and let us know.