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Dear Mayur,
As per the design standards, there are two cases of the material conditions,
1. maximum material condition /(using higher tolerances)/(intersection and penetration occur)
2. minimum material condition/(using lower tolerances)/(gap)
At what material condition you want to simulate your model is important.
To eliminate initial penetration and intersection, you have to simulate it with minimum material condition (with gap)
otherwise you can go to tools menu and auto correct it, but its not good practice to do. you must do it manually.
wherever there is an intersection, please re-mesh that area and check assembly whether components are places properly or not, if not correct it.
or do it in Radioss, with type 24 and allow initial penetration.
Regards,
Ganesh M
Maybe no simple way if it is due to wrong location of components, you have to relocate them