Jérôme Hénin – Software for Biomolecular Simulations

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.

Reference publication for the Colvars Module (open access).

Colvars Dashboard

In development, available from the dashboard branch of the Colvars Git repository.

Distance-to-bound-configuration (DBC) coordinate for affinity calculations

See the JCTC paper: A streamlined, general approach for computing ligand binding free energies and its application to GPCR-bound cholesterol.

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.

VMD extensions and tricks

Qwrap: fast PBC wrapping and unwrapping for VMD

vecexpr: fast vector calcultions for Tcl scripts