CV Documentation

The following list contains descriptions of a number of the colvars that are currently implemented in PLUMED 2.

ALPHABETA	Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values.
ALPHARMSD	Probe the alpha helical content of a protein structure.
ANGLE	Calculate an angle.
ANTIBETARMSD	Probe the antiparallel beta sheet content of your protein structure.
CELL	Calculate the components of the simulation cell
CH3SHIFTS	This collective variable calculates a scoring function based on the comparison of calculated andexperimental methyl chemical shifts.
CONSTANT	Return a constant quantity.
CONTACTMAP	Calculate the distances between a number of pairs of atoms and transform each distance by a switching function.The transformed distance can be compared with a reference value in order to calculate the squared distancebetween two contact maps. Each distance can also be weighted for a given value. CONTACTMAP can be used togetherwith FUNCPATHMSD to define a path in the contactmap space.
COORDINATION	Calculate coordination numbers.
CS2BACKBONE	This collective variable calculates a scoring function based on the comparison of backcalculated andexperimental backbone chemical shifts for a protein (CA, CB, C', H, HA, N).
DHENERGY	Calculate Debye-Huckel interaction energy among GROUPA and GROUPB.
DIHCOR	Measures the degree of similarity between dihedral angles.
DIPOLE	Calculate the dipole moment for a group of atoms.
DISTANCE	Calculate the distance between a pair of atoms.
ENERGY	Calculate the total energy of the simulation box.
FAKE	This is a fake colvar container used by cltools or various other actionsand just support input and period definition
GPROPERTYMAP	Property maps but with a more flexible framework for the distance metric being used.
GYRATION	Calculate the radius of gyration, or other properties related to it.
NOE	Calculates the deviation of current distances from experimental NOE derived distances.
PARABETARMSD	Probe the parallel beta sheet content of your protein structure.
PATHMSD	This Colvar calculates path collective variables.
PATH	Path collective variables with a more flexible framework for the distance metric being used.
PCAVARS	Projection on principal component eigenvectors or other high dimensional linear subspace
POSITION	Calculate the components of the position of an atom.
PROPERTYMAP	Calculate generic property maps.
PUCKERING	Calculate the Nucleic Acid sugar pseudorotation coordinates.
RDC	Calculates the Residual Dipolar Coupling between two atoms.
TEMPLATE	This file provides a template for if you want to introduce a new CV.
TORSION	Calculate a torsional angle.
VOLUME	Calculate the volume of the simulation box.