Count the number of free monomers in simulation box

A free monomer is one with no other monomers within some cut off distance. No, there are only the rigid bodies (monomers).

Sorry for the confusion.

What if you use compute coord/atom with all the “core” particles

assigned a unique type?

You can also use the output of compute cluster/atom as

the input to compute chunk/atom to define one chunk

per cluster. Then you can you fix ave/chunk to tally

the size of each chunk, etc.

See Section howto 6.23.4 example 5 for that very use case.