Collective Variables Module
The Collective Variables Module (Colvars) plugs into molecular dynamics simulation engines such as NAMD and LAMMPS, and the visualization and analysis package VMD. Colvars provides flexible and powerful analysis and biasing on collective variables, including adaptive time-dependent biases. By Giacomo Fiorin (Temple University & NIH) and Jérôme Hénin.
In development, available from the dashboard branch of the Colvars Git repository.
Distance-to-bound-configuration (DBC) coordinate for affinity calculations
Free energy calculations in NAMD: Interleaved Double-Wide Sampling (IDWS)
The feature is briefly documented under alchLambdaIDWS in the NAMD user's guide.
Deinterleaving tool is in development, development version available here.