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 (NIH) and Jérôme Hénin.
Reference publication for the Colvars Module (open access).
Colvars Dashboard: Interactive exploration of Collective Variable space for Molecular Dynamics Simulations
Included in current versions of VMD. Updated versions are available from the Colvars Git repository.
Streamlined Alchemical Free-Energy Perturbation (collab. Grace Brannigan Lab)
See the JCTC paper: A streamlined, general approach for computing ligand binding free energies and its application to GPCR-bound cholesterol and the SAFEP tutorial.
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.