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.

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.
Click on the labels of the actions for more information on what each action computes
noes: NOE ...
GROUPA1the atoms involved in each of the contacts you wish to calculate. =1,3 GROUPB1the atoms involved in each of the contacts you wish to calculate. =2,2 NOEDIST1Add an experimental value for each NOE. =0.6
GROUPA2the atoms involved in each of the contacts you wish to calculate. =5 GROUPB2the atoms involved in each of the contacts you wish to calculate. =7 NOEDIST2Add an experimental value for each NOE. =0.6
GROUPA3the atoms involved in each of the contacts you wish to calculate. =4,4,8,8 GROUPB3the atoms involved in each of the contacts you wish to calculate. =15,16,15,16 NOEDIST3Add an experimental value for each NOE. =0.6
DOSCORE( default=off ) activate metainference
SIGMA_MEAN0 could not find this keyword =1

...
PRINT ARGthe input for this action is the scalar output from one or more other actions. =noes.* FILEthe name of the file on which to output these quantities =colvar

Glossary of keywords and components
Description of components

By default this Action calculates the following quantities. 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 score the Metainference score sigma uncertainty parameter sigmaMean uncertainty in the mean estimate neff effective number of replicas acceptSigma MC acceptance for sigma values noe the # NOE

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

 Quantity Keyword Description acceptScale SCALEDATA MC acceptance for scale value acceptFT GENERIC MC acceptance for general metainference f tilde value weight REWEIGHT weights of the weighted average biasDer REWEIGHT derivatives with respect to the bias scale SCALEDATA scale parameter offset ADDOFFSET offset parameter ftilde GENERIC ensemble average estimator exp NOEDIST 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=10000 ) 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 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 proceeding 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 components 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 REGRES_ZERO stride for regression with zero offset DSIGMA maximum MC move of the uncertainty parameter SIGMA_MEAN0 starting value for the uncertainty in the mean estimate SIGMA_MAX_STEPS Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used TEMP the system temperature - this is only needed if code doesn't pass the temperature to plumed MC_STEPS number of MC steps MC_CHUNKSIZE MC chunksize STATUS_FILE write a file with all the data useful 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...