How to do free energy perturbation

Useful

NAMD

JC made two great tutorials on FEP using NAMD: [1]

1. Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations
2. A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD

Gromacs

Dual topology in Gromacs is a bit tedious. You will need softwares/codes other than Gromacs:

If you mutate between standard amino acids, usually for the purpose of antibody or peptide design, use pmx

Github of pmx

If you mutate between arbitrary chemical compounds/small molecules, usually for the purpose of drug design, use FESetup