common: initial add of md/classical forcefields as discussed in the workshop

Sections added in section_run:

 * section_topology
   * section_atom_type
   * section_molecule_type
     * section_molecule_constraint
     * section_molecule_interaction
   * section_constraint
   * section_interaction
 * section_sampling_method
 * section_frame_sequence
   * section_frame_sequence_user_quantity