Hello everyone, I'm very new in protein KMC/MD and I would like to make the KMC/MD which is based on Breaking-Forming H-bond.

I would like to breaking H-bond from the amino acid residue which have low RMSF after MD production and calculate again for forming H-bond (and for potential energy).

I would like to know that how to create the RMSF cut-off or if someone have a good explaination textbook or paper about Protein KMC/MD procedure

Thank you for your time