Hi everyone,
I am trying to calculate binding free energy of a ligand-protein complex. I have done both simulations
and calculated both energies, now I need free energy of restraints. I have used Gromacs 5.1 version and used couple-moltype and couple-lambdas options in my mdps, and used intermolecular-interactions directive in my topology for restraints (angle, distance and dihedral). Some people recommended me to use equation 14 or 32 from http://pubs.acs.org/doi/abs/10.1021/jp0217839
but I am confused. I have studied this paper 4-5 times and focused on the equations but can't properly get how to use them. If anyone has easy solution or if someone could explain, I will be very grateful.
thanks in advance
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