GROMACS version: 2023
GROMACS modification: No
Dear GROMACS users,
I want to calculate the free energy (alchemical) of relaxing a harmonic potential in a molecule. The restraint between two atoms will force the molecule to stay at one conformation, while gradually relaxing the harmonic potential will let the molecule convert into another conformation.
After I searched the manual and the forum, I think I should use restraint potential (type 10) in the “bonds” section:
[bonds]
; a1 a2 funct lowA up1A up2A kA lowB up1B up2B kB
1 2 10 2.8 2.8 2.8 100000 2.8 2.8 2.8 0
Then, define the “bonded-lambdas” in mdp file to propagate lambda windows:
1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0
Please let me know whether I am doing this right or wrong. Any suggestions are appreciated.