[gmx-users] restraint-lambdas and bonded-lambdas for binding free energy calculations

[Qasim Pars]

Dear users,

I am trying to do the binding free energy calculations. For complex
simulations (Ligand decoupling from complex) I use
"intermolecular_interactions" for Boresch restraints at the end of the
topology file of complex structure:
[ intermolecular_interactions ]
[ bonds ]
...
[ angle_restraints ]
...
[ dihedral_restraints ]
...

I use "coul-lambdas " and "vdw-lambdas" in all the mdp files but I am not
sure whether I also should use "restraint-lambdas" and "bonded-lambdas". My
questions are:
- Should I also use both "restraint-lambdas" and "bonded-lambdas" or one of
them in the mdp files?
- The dihedral_restraints  and  bonds  under intermolecular_interactions
aren't controlled by "restraint-lambdas" and "bonded-lambdas" in the mdp
files, respectively, right?

Thanks in advance,

-- 
Qasim Pars