Collective Variable simulations with the Colvars module

The Colvars module enables on-the-fly computation of low-dimension quantities (collective variables or colvars) in simulations, the application of external forces (biases) to these colvars for restraining or enhanced sampling purposes, and the computation of free energy profiles and other properties. The Colvars library and module are described in ref. 195 as well as in other references that are reported in the log file when the corresponding features are used.

Using Colvars

Colvars simulations are enabled by the following mdp file options: colvars-active, colvars-configfile, and colvars-seed.

Setting colvars-active = true enables Colvars, using a configuration that can be defined by specifying a Colvars configuration file using colvars-configfile.

See this section of the documentation for detailed usage of these options.

Configuration files for input

Colvars configuration files are plain text files describing specific collective variables and biasing and analysis algorithms to be applied onto them. Full documentation is available here.

Additionally, the Colvars Dashboard extension within VMD can be used to prepare a Colvars configuration file, leveraging input templates for many features; VMD version 1.9.4 or later is strongly recommended.

Colvars output files

When Colvars is active, additional output files are written during a GROMACS simulation. Their file names share the same prefix as the edr file, which is ener by default, followed by a suffix specific to their content (e.g. ener.colvars.traj for the trajectory of the collective variables). These files are useful for analysis purposes, but they are not required for continuing a simulation, because the relevant data from Colvars is included in the binary checkpoint file.

Colvars checkpointing

The state of the Colvars library is written to the checkpoint file and read automatically upon restarting.