The following list contains descriptions of a number of the colvars that are currently implemented in the PLUMED-ISDB module. These collective variables are related to the definitions of models to interpret experimental observables. They can be used in combination with any other collective variable, function or bias also outside the ISDB module.
CS2BACKBONE | Calculates the backbone chemical shifts for a protein. |
EMMI | Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. |
FRET | Calculates the FRET efficiency between a pair of atoms.The efficiency is calculated using the Forster relation: |
JCOUPLING | Calculates \(^3J\) coupling constants for a dihedral angle. |
NOE | Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms or ambiguous NOE. |
PCS | Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization. |
PRE | Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms . |
RDC | Calculates the (Residual) Dipolar Coupling between two atoms. |
SAXS | Calculates SAXS scattered intensity using either the Debye equation. |