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. 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 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. 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: JCOUPLING (from PLUMED-ISDB module) Calculates $$^3J$$ coupling constants for a dihedral angle. 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. SAXS (from PLUMED-ISDB module) Calculates SAXS scattered intensity using either the Debye equation or the harmonic sphere approximation.