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If the model already has MMD physics and you want to render animation in Blender, you can:

  • use MMD Physics directly in Blender: click Physics under Model Setup > Assembly. This has performance issue, and it might not work properly. (Link)

  • use physics baking software based on MMD: MMD+MMDBridge, MikuMikuMoving, NexGiMa. The physics will work the best, because it’s MMD. You can import baked physics with VMD.

  • convert physics to cloth sim with MMD Tools Append: