add some comments to the example scripts and move them to the examples/code_fragments dir

examples/code_fragments/mm/1CRN.pdb

examples/code_fragments/mm/ethanol.pdb

examples/code_fragments/mm/ethanol_example.py

examples/code_fragments/mm/ethanol_example_using_topology.py

examples/code_fragments/mm/gb_example.py

examples/code_fragments/mm/gb_example_traj.dcd

examples/code_fragments/mm/gb_example_traj.pdb

examples/code_fragments/mm/gb_example_view_trajectory.py

examples/code_fragments/mm/gb_example_writing_trajectory.py

modules/mol/mm/doc/molmm.rst

modules/mol/mm/examples/1AKI.pdb

modules/mol/mm/examples/1AKI_original.pdb