[gmx-users] Free Energy Methods for Ligand Comparison

[Joanne Hanna]

Hi

I have a system that comprises an enzyme, AMP and Mg2+ cofactor and a phenylalanine ligand, which i have solvated in spc216 waters. I am wanting to calculate the difference in free energy between this system and one in which i have removed this phenylalanine and replaced it with a tyrosine ligand. Although I have read about free energy calculations I am not really sure which method would be best to use, and i'm unsure of how the slow growth method is implemented, any advice would be greatly appreciated.

Many thanks
Jo