FRET

This is part of the isdb module

Calculates 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.

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.

Click on the labels of the actions for more information on what each action computes

fe1: FRET 
ATOMS
the pair of atom that we are calculating the distance between. 
=3,5 
R0
 could not find this keyword 
=5.5 The FRET action with label fe1 calculates a single scalar value
fe2: FRET 
ATOMS
the pair of atom that we are calculating the distance between. 
=2,4 
R0
 could not find this keyword 
=5.5 The FRET action with label fe2 calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=fe1,fe2 The PRINT action with label 

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.

Click on the labels of the actions for more information on what each action computes

WHOLEMOLECULES 
ENTITY0
the atoms that make up a molecule that you wish to align. 
=1-100 The WHOLEMOLECULES action with label 
fe: FRET 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,100 
R0
 could not find this keyword 
=5.5 
NOPBC
( default=off ) ignore the periodic boundary conditions when calculating distances
 The FRET action with label fe calculates a single scalar value
RESTRAINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=fe 
KAPPA
compulsory keyword ( default=0.0 )
specifies that the restraint is harmonic and what the values of the force constants
on each of the variables are 
=100 
AT
compulsory keyword 
the position of the restraint 
=0.5 The RESTRAINT action with label 

Notice that NOPBC is used to be sure that if the distance is larger than half the simulation box the distance is compute properly. Also notice that, since many MD codes break molecules across cell boundary, it might be necessary to use the WHOLEMOLECULES keyword (also notice that it should be before FRET). Just be sure that the ordered list provide to WHOLEMOLECULES has the following properties:

• Consecutive atoms should be closer than half-cell throughout the entire simulation.
• Atoms required later for the distance (e.g. 1 and 100) should be included in the list

Glossary of keywords and components

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