How to do free energy perturbation
Useful
NAMD
JC made two great tutorials on FEP using NAMD: [1]
- Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations
- A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD
Gromacs
There are some great tutorials for calculation of absolute free energy
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
If you mutate between arbitrary chemical compounds/small molecules, usually for the purpose of drug design, use FESetup
