Radius of gyration describes the overall spread of the molecule and is defined as the root mean square distance of the collection of atoms from their common centre of gravity.

There are multiple ways you can do it -

• Use available tools like GROMACS or libraries to compute the radius of gyration directly from the pdb file. Ref1, Ref2
• Write your own script.

In case you want to do it manually, you first need to calculate the center of gravity of the protein and then by iterating over all the atoms in the protein, follow the simple formula mentioned above and calculate the required value.