FRET
 This is part of the colvar module

Calculate the FRET efficiency between a pair of atoms. The efficiency is calculated using the Forster relation:

$E=\frac{1}{1+(R/R_0)^6}$

where $$R$$ is the distance and $$R_0$$ is the Forster radius.

By default the distance is computed taking into account periodic boundary conditions. This behavior can be changed with the NOPBC flag.

The atoms involved can be specified using
 ATOMS the pair of atom that we are calculating the distance between. For more information on how to specify lists of atoms see Groups and Virtual Atoms
Compulsory keywords
 R0 The value of the Forster radius.
Options
 NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances
Examples

The following input tells plumed to print the FRET efficiencies calculated as a function of the distance between atoms 3 and 5 and the distance between atoms 2 and 4.

fe1:  FRET ATOMS=3,5 R0=5.5
fe2:  FRET ATOMS=2,4 R0=5.5
PRINT ARG=fe1,fe2


The following input computes the FRET efficiency calculated on the terminal atoms of a polymer of 100 atoms and keeps it at a value around 0.5.

WHOLEMOLECULES ENTITY0=1-100
fe: FRET ATOMS=1,100 R0=5.5 NOPBC
RESTRAINT ARG=fe KAPPA=100 AT=0.5