Alchemical Free Energy Methods

`Alchemical free energy calculations model the physically impossible but
computationally realizable process of gradually mutating a subset of atoms of a
system from one state to another, through a series of intermediate steps. Two
alternative methods for alchemical calculation of free energies from molecular
dynamics simulation are available in NAMD: Free energy perturbation (FEP) and
thermodynamic integration (TI).
`

- Theoretical Background

- Implementation of the free energy methods in NAMD
- Examples of input files for running alchemical free energy calculations
- Description of a free energy calculation output

http://www.ks.uiuc.edu/Research/namd/