NOE
 This is part of the colvar module

Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms or ambiguous NOE.

Each NOE is defined by two groups containing the same number of atoms, distances are calculated in pairs, transformed in 1/r^6, summed and saved as components.

$NOE() = (\frac{1}{N_{eq}}\sum_j^{N_{eq}} (\frac{1}{r_j^6}))^{\frac{-1}{6}}$

Intensities can then in principle ensemble averaged using ENSEMBLE and used to calculate a scoring function for example with METAINFERENCE.

Description of components

The names of the components in this action can be customized by the user in the actions input file. However, in addition to these customizable components the following quantities will always be output

 Quantity Description noe the # NOE

In addition the following quantities can be calculated by employing the keywords listed below

 Quantity Keyword Description exp ADDEXP the # NOE experimental distance
The atoms involved can be specified using
 GROUPA the atoms involved in each of the contacts you wish to calculate. Keywords like GROUPA1, GROUPA2, GROUPA3,... should be listed and one contact will be calculated for each ATOM keyword you specify. You can use multiple instances of this keyword i.e. GROUPA1, GROUPA2, GROUPA3... GROUPB the atoms involved in each of the contacts you wish to calculate. Keywords like GROUPB1, GROUPB2, GROUPB3,... should be listed and one contact will be calculated for each ATOM keyword you specify. You can use multiple instances of this keyword i.e. GROUPB1, GROUPB2, GROUPB3...
Options
 NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances ADDEXP ( default=off ) Set to TRUE if you want to have fixed components with the experimental reference values. NOEDIST Add an experimental value for each NOE. You can use multiple instances of this keyword i.e. NOEDIST1, NOEDIST2, NOEDIST3...
Examples

In the following examples three noes are defined, the first is calculated based on the distances of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances 4-15,4-16,8-15,8-16.

NOE ...
GROUPA1=1,3 GROUPB1=2,2
GROUPA2=5 GROUPB2=7
GROUPA3=4,4,8,8 GROUPB3=15,16,15,16
LABEL=noes
... NOE

PRINT ARG=noes.* FILE=colvar