Here is an excerpt from my input file that dumps the per-molecule values you were asking about.
compute GYRm gps gyration/molecule
compute COMm gps com/molecule
fix GYRm gps ave/time 500 1 500 c_GYRm c_COMm c_COMm c_COMm mode vector file GYRmol.ave
See http://lammps.sandia.gov/doc/fix_ave_time.html for info on the ‘fix ave/time’ command.
Graduate Research Associate
Department of Mechanical Engineering
The Ohio State University