1. data - input data file
2. atomgroups - input file specifying group rotation moves: axis of rotation,
group members, selection probability and maximum rotation amplitude of each group
3. coords.inpcrd - the initial coordinates of the peptide
4. coords.prmtop - the topology/parameter file for the peptide
5. rbodyconfig - sets of atoms grouped as local rigid bodies
6. coordsinirigid - the reference coordinates of the atoms in the rigid bodies
7. min.in - AMBER's parameter file for minimization
8. min_md.in - AMBER's parameter file for molecular dynamics runs
9. OUTPUT_FILES directory - output files generated by the GMIN program

Notes: 
1. use the keyword RIGIDINIT in the data file if local rigid body is employed
2. remove the keyword RIGIDINIT otherwise