The following list contains descriptions of a number of the colvars that are currently implemented in PLUMED.
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 |
CONSTANT | Return one or more constant quantitieswith or without derivatives. |
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 the backbone chemical shifts for a protein. |
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_FROM_CONTOUR | Calculate the perpendicular distance from a Willard-Chandler dividing surface. |
DISTANCE | Calculate the distance between a pair of atoms. |
ENERGY | Calculate the total energy of the simulation box. |
ERMSD | Calculate eRMSD with respect to a reference structure. |
FAKE | This is a fake colvar container used by cltools or various other actionsand just support input and period definition |
FRET | Calculate the FRET efficiency between a pair of atoms.The efficiency is calculated using the Forster relation: |
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. |
JCOUPLING | Calculates \(^3J\) coupling constants for a dihedral angle. |
NOE | Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atomsor ambiguous NOE. |
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. |
PRE | Calculates the Paramegnetic Resonance Enhancement intensity ratio between two atoms.The reference atom for the spin label is added with SPINLABEL, the affected atom(s)are give as numbered GROUPA1, GROUPA2, ...The additional parameters needed for the calculation are given as INEPT, the inepttime, TAUC the correlation time, OMEGA, the larmor frequency and RTWO for the relaxationtime. |
PROPERTYMAP | Calculate generic property maps. |
PUCKERING | Calculate 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. |