Collective Variable-based Calculations (Colvars)

The features described in this section were originally contributed to NAMD by Giacomo Fiorin (NIH) and Jérôme Hénin (CNRS, France) and are currently developed at this external repository:
`https://github.com/Colvars/colvars`

An updated version of this section can also be downloaded as a separate manual:

HTML: `https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html`

PDF: `https://colvars.github.io/pdf/colvars-refman-namd.pdf`

See section 9.7 for specific changes that affect compatibility between versions. Please ask any usage questions through the NAMD mailing list, and development questions through GitHub.

- Overview
- Writing a Colvars configuration: a crash course
- Enabling and controlling the Colvars module in NAMD
- Units in the Colvars module
- NAMD parameters
- Using the
`cv`command to control the Colvars module - Configuration syntax used by the Colvars module
- Global keywords
- Input state file
- Output files

- Defining collective variables
- Choosing a function
- Distances
`distance`: center-of-mass distance between two groups.`distanceZ`: projection of a distance vector on an axis.`distanceXY`: modulus of the projection of a distance vector on a plane.`distanceVec`: distance vector between two groups.`distanceDir`: distance unit vector between two groups.`distanceInv`: mean distance between two groups of atoms.

- Angles
- Contacts
- Collective metrics
`rmsd`: root mean square displacement (RMSD) from reference positions.- Advanced usage of the
`rmsd`component. `eigenvector`: projection of the atomic coordinates on a vector.`gyration`: radius of gyration of a group of atoms.`inertia`: total moment of inertia of a group of atoms.`dipoleMagnitude`: dipole magnitude of a group of atoms.`inertiaZ`: total moment of inertia of a group of atoms around a chosen axis.

- Rotations
`orientation`: orientation from reference coordinates.`orientationAngle`: angle of rotation from reference coordinates.`orientationProj`: cosine of the angle of rotation from reference coordinates.`spinAngle`: angle of rotation around a given axis.`tilt`: cosine of the rotation orthogonal to a given axis.

- Protein structure descriptors
- Raw data: building blocks for custom functions
- Geometric path collective variables
`gspath`: progress along a path defined in atomic Cartesian coordinate space.`gzpath`: distance from a path defined in atomic Cartesian coordinate space.`linearCombination`: Helper CV to define a linear combination of other CVs`gspathCV`: progress along a path defined in CV space.`gzpathCV`: distance from a path defined in CV space.

- Arithmetic path collective variables
- Volumetric map-based variables
- Shared keywords for all components
- Periodic components
- Non-scalar components
- Linear and polynomial combinations of components
- Custom functions
- Scripted functions
- Defining grid parameters
- Trajectory output
- Extended Lagrangian
- Multiple time-step variables
- Backward-compatibility
- Statistical analysis

- Selecting atoms
- Atom selection keywords
- Moving frame of reference.
- Treatment of periodic boundary conditions.
- Performance of a Colvars calculation based on group size.

- Biasing and analysis methods
- Thermodynamic integration
- Adaptive Biasing Force
- Extended-system Adaptive Biasing Force (eABF)
- Metadynamics
- Harmonic restraints
- Computing the work of a changing restraint
- Harmonic wall restraints
- Linear restraints
- Adaptive Linear Bias/Experiment Directed Simulation
- Multidimensional histograms
- Probability distribution-restraints
- Defining scripted biases
- Performance of scripted biases

- Scripting interface (Tcl): list of commands
- Commands to manage the Colvars module
- Commands to manage individual collective variables
- Commands to manage individual biases

- Syntax changes from older versions

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