The typical fragment move is the replacement of torsion angles for a stretch of consecutive residues with torsion angles stored in the fragment library. Moves of this kind are sampled by applying objects of the type FragmentMover to the Pose.
The fragment library is prepared for a specific protein and is position specific. The standard abrelax protocol uses the first 200 3mer fragments stored in a 3-mer fragment library and the first 25 9mer fragments stored in the respective 9mer library. The fragment libraries are given using the flags (-abinitio:frags3 and -abinitio:frags9). The protocol, however, doesn't care about the exact size of the fragments such that the same flags ( or their alias -abinitio:frags_small -abinitio:frags_large ) can be used to give any type of fragment library. The 9mer or large fragments are used during abinitio stages I-III and the 3-mer or smaller fragments are used during stage IV to achieve more fine-grained sampling.
Note, that the default behavior of the fragment_picker is to generate 200 fragments of each size (3mers and 9mers) such that the lower ranking 175 9mer fragments are ignored. If you wish to included all fragments in your fragment library, regardless, you can use the flags ( -abinitio:number_9mer_frags 0 ).
It is important to be aware that the fragment picking process can pick fragments of homologous protein structures. If you are using ROSETTA to model an unknown structure it is of course an advantage if homologous information is available and you can keep the homologous fragments. If, however, you are benchmarking a protocol to get a feeling how well ROSETTA works, or to develop new protocols, you may want to remove homologous fragments.