[gmx-users] free energy settings

[Qasim Pars]

Dear users,

I have a few questions about the below free energy settings:

;State A
free-energy              = yes
init-lambda              = 0
delta-lambda             = 0
sc-alpha                 = 0.5
sc-power                 = 1
sc-sigma                 = 0.3
couple-intramol          = no
couple-lambda0           = vdw-q
couple-lambda1           = none
couple-moltype           = ligand

According to the above settings the ligand in the state A will stay in the
protein binding pocket. For state A the ligand has bonded and non-bonded
interactions with the protein, right? Whereas I set/turn on only the
non-bonded interactions (couple-lambda0 = vdw-q) but I couldn't find any
command to turn on the bonded interactions for the state A. Is there any
command to turn on the bonded interactions in GROMACS2016?

;State B
free-energy              = yes
init-lambda              = 1
delta-lambda             = 0
sc-alpha                 = 0.5
sc-power                 = 1
sc-sigma                 = 0.3
couple-intramol          = no
couple-lambda0           = vdw-q
couple-lambda1           = none
couple-moltype           = ligand

As for state B the ligand doesn't have both bonded and non-bonded
interactions with the protein, right? Therefore the ligand in the state B
probably will move out from the protein binding pocket. Is this an expected
result?

I think for both two states the topology file can just be a normal topology
as in a protein-ligand simulation. The ligand does not need to be a residue
of the protein, and there is not need to have a state B defined in the
topology file, as the couple- flags in the mdp already build the B state
for the decoupled ligand automatically. Am I wrong?

Thanks in advance

-- 
Qasim Pars