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

- Overview
- A crash course
- General parameters

- Defining collective variables
- Choosing a function
`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.`distancePairs`: set of pairwise distances between two groups.`cartesian`: vector of atomic Cartesian coordinates.`angle`: angle between three groups.`dipoleAngle`: angle between two groups and dipole of a third group.`dihedral`: torsional angle between four groups.`polarTheta`: polar angle in spherical coordinates.`polarPhi`: azimuthal angle in spherical coordinates.`coordNum`: coordination number between two groups.`selfCoordNum`: coordination number between atoms within a group.`hBond`: hydrogen bond between two atoms.`rmsd`: root mean square displacement (RMSD) from reference positions.- Advanced usage of the
`rmsd`component. - Path collective variables
`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.`inertiaZ`: total moment of inertia of a group of atoms around a chosen axis.`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.`alpha`: -helix content of a protein segment.`dihedralPC`: protein dihedral pricipal component

- 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
- Backward-compatibility
- Statistical analysis

- Choosing a function
- 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
- 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

- Syntax changes from older versions

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