Are you using bonded contact between flanges? Ideally, it should be frictional.
- Underside of the bolt head to flange
- Underside of Nut to Flange
- Nut to Bolt
above three contacts should be bonded. Also, is your bolt shank cylindrical? If yes, simply take an imprint of nuts on the bolt and apply pretension on the cylindrical face between nut and bolt head. This way you will not have to worry about coordinate systems definitions.
-Aniket
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