Thank you for the feedback!
In my experience, fix rigid/small does work for adding rigid molecules on the fly as specified by a molecule template file, and it does indicate that an infile should be able to store the centers of masses - here is the section of the documentation in question:
IMPORTANT NOTE: If you are using fix rigid/small and defining a system that has no rigid bodies initially, because they will be added on-the-fly by commands such as fix deposit or fix pour, you may still wish to use the infile keyword. This is so that restart files written during the simulation will output an auxiliary restart file as described above with information on the new rigid bodies. In this case the initial infile file should use N = 0.
I have tried this (having an infile that contains only “N=0” and no other lines), but I am unable to get this functionality to work.
Again, thank you,