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. |
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 quantities with or without derivatives. |
CONTACTMAP | Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. |
COORDINATION | Calculate coordination numbers. |
DHENERGY | Calculate Debye-Huckel interaction energy among GROUPA and GROUPB. |
DIHCOR | Measures the degree of similarity between 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. |
DISTANCE | Calculate the distance between a pair of atoms. |
DISTANCE_FROM_CONTOUR | Calculate the perpendicular distance from a Willard-Chandler dividing surface. |
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 |
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. |
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. |
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 |
POSITION | Calculate the components of the position of an atom. |
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. |
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. |
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. |
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. |