[gmx-users] topology for free energy by perturbation

[Mikko Huhtala]

I'm not at all familiar with free energy perturbation
calculations. I'd like to calculate the free energy difference between
two small-molecule ligand complexes of a protein. The difference
between the ligands is a replacement of one -OH group with
-NH+(CH3)2. Is this too big a difference for perturbation? If not, how
should the topology be constructed? Can dummy atoms be added to the
-OH group and then be perturbed into -CH3s?

Mikko