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 |

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. |

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. |

S2CM | (from S2 contact model collective variable module) S2 contact model CV used in [96], based on NH order parameter from [139] and methyl order parameter from [88]. Input parameters can be found in the relevant papers. |

SASA_HASEL | (from SASA collective variable module) Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The algorithm described in [62] is used for the calculation. The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of SASA is updated (the default is every 10 steps). |

SASA_LCPO | (from SASA collective variable module) Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The LCPO algorithm is used for the calculation (please, read and cite [135]). The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of the SASA is updated (the default is every 10 steps). |

SAXS | (from PLUMED-ISDB module) Calculates SAXS scattered intensity using either the Debye equation. |