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
- 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/