AFMM is currently implemented for CHARMM and AMBER force fields. Our software cannot handle the Gromacs force field because it is united-atom and therefore matching QMM and MM normal modes does not make much sense.
You can find more information about AFMM here:
Z. Cournia, J. C. Smith, and G. M. Ullmann (2005) A molecular mechanics force-field for biologically-important sterols. J. Comp. Chem., 26:1383-1399.
A. C. Vaiana, Z. Cournia, I. B. Costescu, and J. C. Smith (2005) AFMM: A molecular mechanics force-field vibrational parametrization program. Comput. Phys. Commun., 167:34-42.
Please email me at: zcournia [at] bioacademy.gr if you are interested in receiving the code, the manual and support.