means total PE of system * Natoms (in system) / Natomsbig (# of big atoms)
pe and atoms are thermo keywords (see the thermo_style command)
When this script does thermo output quantities are divided by Natoms
(default for LJ units), settable by themo_modify norm.
So you will effectively get the PE/big-atom, in an average sense.
If you want to sum the pe/atom for just big atoms, see the compute
reduce command. Or compute ke/atom or variable group function ke(group)
You can just use compute msd for a group of atoms (e.g. big). See its doc
page for an explanation.