Action: FRET

Module	isdb
Description	Usage
Calculates the FRET efficiency between a pair of atoms.
output value	type
the fret efficiency between the input pair of atoms	scalar

Details and examples

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

fe1The FRET action with label fe1 calculates the following quantities:
 Quantity   
 Type   
 Description  
fe1
scalar
the fret efficiency between the input pair of atoms:  FRETCalculates the FRET efficiency between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,5 R0The value of the Forster radius=5.5
fe2The FRET action with label fe2 calculates the following quantities:
 Quantity   
 Type   
 Description  
fe2
scalar
the fret efficiency between the input pair of atoms:  FRETCalculates the FRET efficiency between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,4 R0The value of the Forster radius=5.5
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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.

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

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-100
The WHOLEMOLECULES action with label  calculates somethingfeThe FRET action with label fe calculates the following quantities:
 Quantity   
 Type   
 Description  
fe
scalar
the fret efficiency between the input pair of atoms: FRETCalculates the FRET efficiency between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,100 R0The value of the Forster radius=5.5 NOPBC ignore the periodic boundary conditions when calculating distances
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=fe KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100 ATthe position of the restraint=0.5

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

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ATOMS	atoms	the pair of atom that we are calculating the distance between

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ATOMS	input	none	the pair of atom that we are calculating the distance between
R0	compulsory	none	The value of the Forster radius
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOPBC	optional	false	ignore the periodic boundary conditions when calculating distances