GROMACS version: 2021.4
GROMACS modification: Yes (PLUMED patch)
I am trying to calculate free energy of a system where one ligand molecule is stuck inside protein fibril and one outside the fibril. The inner ligand’s vdw force becomes zero and the outer becomes a non-zero value over lambda steps.
I have tried the same kind of simulation with a simple O2 molecule by implementing a dummy molecule and adding fep_lambdas option to mdp files and suceeded. However, this doesn’t work for the current protein-ligand system. The ligand has more than 20 heavy atoms, which I guess it makes harder for the dummy molcule to work.
Does anyone have a good idea for my system simpler than using a dummy molcule fep_lambdas?