There is nothing special about a plugin vs the main code. The neighbor list is a class and it will compute the neighbor list you request via the API calls. You don't provide much information, so I can only guess at what the issue might be.
My best guess is that you are using the same neighbor list class instance for the pair potentials and your plugin. I would guess that your plugin doesn't not provide r_cut values to the neighbor list. Each neighbor list instance finds neighbors within the maximum r_cut from all registered consumer class instances.
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
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