NOE
This is part of the isdb 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.

\[ NOE() = (\frac{1}{N_{eq}}\sum_j^{N_{eq}} (\frac{1}{r_j^6})) \]

NOE can be used to calculate a Metainference score over one or more replicas using the intrinsic implementation of METAINFERENCE that is activated by DOSCORE.

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
sigma uncertainty parameter
sigmaMean uncertainty in the mean estimate
acceptSigma MC acceptance
noe the # NOE

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

Quantity Keyword Description
acceptScale SCALEDATA MC acceptance
weight REWEIGHT weights of the weighted average
biasDer REWEIGHT derivatives wrt the bias
scale SCALEDATA scale parameter
offset ADDOFFSET offset parameter
ftilde GENERIC ensemble average estimator
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...
Compulsory keywords
NOISETYPE ( default=MGAUSS ) functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
LIKELIHOOD ( default=GAUSS ) the likelihood for the GENERIC metainference model, GAUSS or LOGN
DFTILDE ( default=0.1 ) fraction of sigma_mean used to evolve ftilde
SCALE0 ( default=1.0 ) initial value of the scaling factor
SCALE_PRIOR ( default=FLAT ) either FLAT or GAUSSIAN
OFFSET0 ( default=0.0 ) initial value of the offset
OFFSET_PRIOR ( default=FLAT ) either FLAT or GAUSSIAN
SIGMA0 ( default=1.0 ) initial value of the uncertainty parameter
SIGMA_MIN ( default=0.0 ) minimum value of the uncertainty parameter
SIGMA_MAX ( default=10. ) maximum value of the uncertainty parameter
OPTSIGMAMEAN ( default=NONE ) Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
WRITE_STRIDE ( default=1000 ) write the status to a file every N steps, this can be used for restart/continuation
Options
NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically
DOSCORE ( default=off ) activate metainference
NOENSEMBLE ( default=off ) don't perform any replica-averaging
REWEIGHT ( default=off ) simple REWEIGHT using the ARG as energy
SCALEDATA ( default=off ) Set to TRUE if you want to sample a scaling factor common to all values and replicas
ADDOFFSET ( default=off ) Set to TRUE if you want to sample an offset common to all values and replicas
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.

ARG the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three componets x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...
AVERAGING Stride for calculation of averaged weights and sigma_mean
SCALE_MIN minimum value of the scaling factor
SCALE_MAX maximum value of the scaling factor
DSCALE maximum MC move of the scaling factor
OFFSET_MIN minimum value of the offset
OFFSET_MAX maximum value of the offset
DOFFSET maximum MC move of the offset
DSIGMA maximum MC move of the uncertainty parameter
SIGMA_MEAN0 starting value for the uncertainty in the mean estimate
TEMP the system temperature - this is only needed if code doesnt' pass the temperature to plumed
MC_STEPS number of MC steps
MC_STRIDE MC stride
MC_CHUNKSIZE MC chunksize
STATUS_FILE write a file with all the data usefull for restart/continuation of Metainference
SELECTOR name of selector
NSELECT range of values for selector [0, N-1]
RESTART allows per-action setting of restart (YES/NO/AUTO)
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. METAINFERENCE is activated using DOSCORE.
NOE ...
GROUPA1=1,3 GROUPB1=2,2
GROUPA2=5 GROUPB2=7
GROUPA3=4,4,8,8 GROUPB3=15,16,15,16
DOSCORE
LABEL=noes
... NOE

PRINT ARG=noes.* FILE=colvar