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Cloning Soft Body Dynamics without breaking your system

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So the basic setup is a bunch of cloned spheres, which inflate inside a capsule object and are supposed to vaguely simulate cell movement inside a Mitochondria.



But I want this effect to be cloned, so I can later animate them with effectors.




As you might imagine, doing so will absolutely break my system. I got a pretty alright system (Nvidia 1070Ti, Ryzen 3700X, 32Gb Ram) altough it could probably be better. The moment I clone everything, it just freezes


So I guess the question is, how would I go about this?


Thank you in advance for any help.

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