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Please refer this video and let me know why my skeleton moves slightly up and down during simulation? I have done the mass and COM adjustments also.
https://youtu.be/HvTy0cGNiPk

Do you have two separate ground reaction forces, applying one to each foot?

yes sir, I have 2 seperate GRFS.

I've had odd movements in the y axis myself, but I haven't had GRFs taken into account at any point - just a model (that has an associated motion) that is scaled with the original's motion applied to it. For me, the movement is more of a compression than a drifting as in OP's.

What other possibilities are there?

James Dunne, Can you tell us the reason behind this?

The reason is simple; all of the forces, masses are not in equilibrium. 'Why' can be due to a number of things.

Maybe you didn't apply your external forces correctly, maybe the masses are not correct, maybe the residual actuators are not being applied appropriately.

Have you run Inverse Dynamics and assessed if the joint torques and residuals are what you expect?

I would suggest working through this example. In Part II of the example, you iterate on a Model in RRA to reduce the 'bouncing' and achieve a 'good' simulation.

-j