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I am using OpenSim 4.4 and am having issues with my external forces. I have written a .mot file in MATLAB for a person cycling (looking at only grf for feet at the moment) based off torque data and moment arms etc. This has given me a ground_force_vy and a l_ground_force_vy. All other forces an torques have been written as 0 for the entire time duration. I have set force to be applied to the body (I want the ground reaction force to follow each foot at a perpendicular orientation throughout the cycling motion). When I upload this into my external force setup for inverse dynamics, applying the force to the calcn_r and calcn_l, I get an associated motion from my .mot file which is floating beneath the person cycling, in the middle of the two legs. It seems to move up and down slightly (in the y-axis) and there seems to only be the one force (or they overlap completely despite having very different forces). Does anybody know how to resolve this or where the major issues may lie. The magnitude seems to be reasonable.
I have attached the .mot file and external forces setup file.

I think what u mean is your grf is not consistent with your IK.mot results that is the grf is not applied at the correct points of application. So i guess u need to check your COP calculations. I had similar issues and the COP calculation was wrong.