cmdata: implement group selection

[carlocamilloni]

if you have a tpr with more molecules (eg solvent) and try to select only protein it hangs or fail

[carlocamilloni]

with the new cmdata group selection is not included so does not give errors. If we want to implement it I think it should only focus on giving the possibility to select subset of molecules and not subset of atoms, otherwise the output interpretation by make_mat could become too complicated