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.
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: FRETATOMS=3,5the pair of atom that we are calculating the distance between.R0=5.5 fe2: FRETcould not find this keywordATOMS=2,4the pair of atom that we are calculating the distance between.R0=5.5 PRINTcould not find this keywordARG=fe1,fe2compulsory keyword the labels of the values that you would like to print to the file
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.
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:
By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.
Quantity | Description |
.#!value | the fret efficiency between the input pair of atoms |
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 |
R0 | The value of the Forster radius. |
NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |