CV Documentation

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

ADAPTIVE_PATH Compute path collective variables that adapt to the lowest free energy path connecting states A and B.
ALPHARMSD Probe the alpha helical content of a protein structure.
ANGLE Calculate an angle.
ANGLES Calculate an angle.
ANGLE_SCALAR Calculate an angle.
ANGLE_VECTOR Calculate multiple angles.
ANTIBETARMSD Probe the antiparallel beta sheet content of your protein structure.
BETWEEN_MATRIX Transform all the elements of a matrix using a switching function that is oen when the input value is within a particular range
BOPS Calculate the BOPS order parameter
CELL Calculate the components of the simulation cell
COMBINE_MATRIX Calculate the sum of a number of matrices
CONSTANT Create a constant value that can be passed to actions
CONTACTMAP Calculate the distances between a number of pairs of atoms and transform each distance by a switching function.
COORDINATION Calculate coordination numbers.
CUSTOM_MATRIX Calculate an arbitrary function piecewise for one or multiple input matrices.
DHENERGY Calculate Debye-Huckel interaction energy among GROUPA and GROUPB.
DIHCOR Measures the degree of similarity between dihedral angles.
DIHEDRAL_CORRELATION Measure the correlation between a pair of dihedral angles
DIHEDRAL_CORRELATION_SCALAR Measure the correlation between a multiple pairs of dihedral angles
DIHEDRAL_CORRELATION_VECTOR Measure the correlation between a multiple pairs of dihedral angles
DIMER This CV computes the dimer interaction energy for a collection of dimers.
DIPOLE Calculate the dipole moment for a group of atoms.
DIPOLE_SCALAR Calculate the dipole moment for a group of atoms.
DISTANCE Calculate the distance between a pair of atoms.
DISTANCE_FROM_CONTOUR Calculate the perpendicular distance from a Willard-Chandler dividing surface.
DISTANCE_FROM_SPHERICAL_CONTOUR Calculate the perpendicular distance from a Willard-Chandler dividing surface.
DOPS Calculate the DOPS order parameter
EEFSOLV Calculates EEF1 solvation free energy for a group of atoms.
ENERGY Calculate the total potential energy of the simulation box.
ERMSD Calculate eRMSD with respect to a reference structure.
EXTRACV Allow PLUMED to use collective variables computed in the MD engine.
FAKE This is a fake colvar container used by cltools or various other actions that supports input and period definitions
GEOMETRIC_PATH Distance along and from a path calculated using geometric formulas
GHBFIX Calculate the GHBFIX interaction energy among GROUPA and GROUPBusing a potential defined in Kührová et al., Improving the performance of the AMBER RNA force field bytuning the hydrogen-bonding interactions, JCTC, 2019. Essentially it is a switching function being -1 for small distances and 0 for large distances with a smooth interpolation in the middle. This can be scaled as desired by specifying interaction scaling parameters and energy units.
GPATH Distance along and from a path calculated using geometric formulas
GPROPERTYMAP Property maps but with a more flexible framework for the distance metric being used.
GSYMFUNC_THREEBODY Calculate functions of the coordinates of the coordinates of all pairs of bonds in the first coordination sphere of an atom
GYRATION Calculate the radius of gyration, or other properties related to it.
GYRATION_FAST Calculate the radius of gyration, or other properties related to it.
HBPAMM_SA Calculate the number of hydrogen bonds each acceptor participates in using the HBPamm method
HBPAMM_SD Calculate the number of hydrogen bonds each donor participates in using the HBPamm method
HBPAMM_SH Calculate the number of hydrogen bonds each hydrogen participates in using the HBPamm method
HIGHEST_SCALAR Calculate the highest of a set of sclalar arguments
HIGHEST_VECTOR Calculate the largest element in a vector of inputs
LESS_THAN_MATRIX Transform all the elements of a matrix using a switching function that is one when the input value is smaller than a threshold
LOWEST_SCALAR Calculate the lowest of a set of sclalar arguments
LOWEST_VECTOR Calculate the lowest element in a vector of inputs
MATHEVAL_MATRIX Calculate an arbitrary function piecewise for one or multiple input matrices.
MEAN Calculate the arithmetic mean of the elements in a vector
MEAN_SCALAR Calculate the arithmetic mean of the set of input scalars
MEAN_VECTOR Calculate the arithmetic mean of the elements in a vector
MORE_THAN_MATRIX Transform all the elements of a matrix using a switching function that is one when the input value is larger than a threshold
ONES Create a constant vector with all elements equal to one
OUTER_PRODUCT Calculate the outer product matrix of two vectors
PARABETARMSD Probe the parallel beta sheet content of your protein structure.
PATH Path collective variables with a more flexible framework for the distance metric being used.
PATHMSD This Colvar calculates path collective variables.
PCAVARS Projection on principal component eigenvectors or other high dimensional linear subspace
PDB2CONSTANT Create a constant value from a PDB input file
PLANE Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule.
PLANE_SCALAR Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule.
PLANE_VECTOR Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule multiple times.
POSITION Calculate the components of the position of an atom.
POSITION_SCALAR Calculate the components of the position of an atom.
POSITION_VECTOR Create a vector that holds the components of the position of a set of atoms.
PROJECTION_ON_AXIS Calculate a position based on the projection along and extension from a defined axis.
PROPERTYMAP Calculate generic property maps.
PUCKERING Calculate sugar pseudorotation coordinates.
PYCVINTERFACE Define collective variables in the Python language.
QUATERNION Calculate quaternions for molecules.
QUATERNION_SCALAR Calculate a single quaternion
QUATERNION_VECTOR Calculate multiple quaternions
ROPS Calculate the ROPS order parameter
SUM Calculate the sum of the arguments
SUM_MATRIX Sum all the elements in a matrix
SUM_SCALAR Calculate the SUM of the set of input scalars
SUM_VECTOR Calculate the sum of the elements in a vector
TEMPLATE This file provides a template for if you want to introduce a new CV.
TORSION Calculate a torsional angle.
TORSION_SCALAR Calculate a torsional angle.
VOLUME Calculate the volume of the simulation box.
XANGLES Calculate the angle between an arbitrary vector and the positive x direction
XYTORSIONS Calculate the torsional angle around the x axis between an arbitrary vector and the positive y direction
XZTORSIONS Calculate the torsional angle around the x axis between an arbitrary vector and the positive z direction
YANGLES Calculate the angle between an arbitrary vector and the positive y direction
YXTORSIONS Calculate the torsional angle around the y axis between an arbitrary vector and the positive x direction
YZTORSIONS Calculate the torsional angle around the y axis between an arbitrary vector and the positive z direction
ZANGLES Calculate the angle between an arbitrary vector and the positive z direction
ZXTORSIONS Calculate the torsional angle around the z axis between an arbitrary vector and the positive x direction
ZYTORSIONS Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction

In addition to the keywords above, by enabling optional modules you can access to the following keywords:

CS2BACKBONE (from PLUMED-ISDB module) Calculates the backbone chemical shifts for a protein.
EMMI (from PLUMED-ISDB module) Calculate the fit of a structure or ensemble of structures with a cryo-EM density map.
EMMIVOX (from PLUMED-ISDB module) Bayesian single-structure and ensemble refinement with cryo-EM maps.
FRET (from PLUMED-ISDB module) Calculates the FRET efficiency between a pair of atoms.The efficiency is calculated using the Forster relation:
FUNNEL_PS (from Funnel-Metadynamics (FM) module) FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2.
FUSIONPOREEXPANSIONP (from Membrane Fusion module) A CV for inducing the expansion of a fusion pore from a nucleated fusion pore.
FUSIONPORENUCLEATIONP (from Membrane Fusion module) A CV for inducing the nucleation of the fusion pore from a hemifusion stalk.
JCOUPLING (from PLUMED-ISDB module) Calculates \(^3J\) coupling constants for a dihedral angle.
MEMFUSIONP (from Membrane Fusion module) Calculate a CV that can induce the formation of the hemifusion stalk between two initially flat and planar bilayers.
NOE (from PLUMED-ISDB module) Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms or ambiguous NOE.
PCS (from PLUMED-ISDB module) Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization.
PIV (from PIV collective variable module) Calculates the PIV-distance.
PRE (from PLUMED-ISDB module) Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms .
RDC (from PLUMED-ISDB module) Calculates the (Residual) Dipolar Coupling between two atoms.
S2CM (from S2 contact model collective variable module) S2 contact model CV.
SANS (from PLUMED-ISDB module) Calculates SANS intensity.
SASA_HASEL (from SASA collective variable module) Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it.
SASA_LCPO (from SASA collective variable module) Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it.
SAXS (from PLUMED-ISDB module) Calculates SAXS intensity.
SHADOW (from PLUMED-ISDB module) Communicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation.