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

- Hybrid single-dual topology approach for relative binding free energy calculation of ligand to receptor

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