The first step in creating the MD file is to set up the machine hierarchy, which is done using the Parent/Child Relationships dialog. You must add all components that you want to show during machine simulation as children of machine in the Part View. The main purpose of this is to create a hierarchy of movement, but static components (such as body, base, or even logos) are also included. There may be solids that you choose to leave in the document even though they are not displayed during simulation (for example the doors, which should always be hidden during simulation, or a parts-catcher mechanism for which you plan to add the simulation at a later time).
Here are examples of two different machines with their parent/child relationships structures set up.
Turn/mill example:
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5-axis milling example:
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In the turn/mill example, the jaws are children of the chucks, which are children of the heads. In the mill example, head sits on the z_slide, which sits on the x_slide.
Additional notes