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:FRETATOMS=3,5the pair of atom that we are calculating the distance between.R0=5.5could not find this keywordfe2:FRETATOMS=2,4the pair of atom that we are calculating the distance between.R0=5.5 PRINTcould not find this keywordARG=the input for this action is the scalar output from one or more other actions.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

WHOLEMOLECULESENTITY0=1-100the atoms that make up a molecule that you wish to align.fe:FRETATOMS=1,100the pair of atom that we are calculating the distance between.R0=5.5could not find this keywordNOPBCRESTRAINT( default=off ) ignore the periodic boundary conditions when calculating distancesARG=the input for this action is the scalar output from one or more other actions.feKAPPA=100compulsory keyword ( default=0.0 )specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=0.5compulsory keywordthe position of the restraint

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 |