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 ...
   
GROUPA1
the atoms involved in each of the contacts you wish to calculate. 
=1,3 
GROUPB1
the atoms involved in each of the contacts you wish to calculate. 
=2,2 
NOEDIST1
Add an experimental value for each NOE.. 
=0.6 
   
GROUPA2
the atoms involved in each of the contacts you wish to calculate. 
=5 
GROUPB2
the atoms involved in each of the contacts you wish to calculate. 
=7 
NOEDIST2
Add an experimental value for each NOE.. 
=0.6 
   
GROUPA3
the atoms involved in each of the contacts you wish to calculate. 
=4,4,8,8 
GROUPB3
the atoms involved in each of the contacts you wish to calculate. 
=15,16,15,16 
NOEDIST3
Add an experimental value for each NOE.. 
=0.6 
   
DOSCORE
( default=off ) activate metainference 
 
   
SIGMA_MEAN0
 could not find this keyword 
=1 
   
...The NOE action with label noes calculates the following quantities:

 Quantity   
 Description  
noes.noe-0
the # NOE  This is the 0th of these quantities
noes.noe-1
the # NOE  This is the 1th of these quantities
noes.noe-2
the # NOE  This is the 2th of these quantities
noes.exp-0
the # NOE experimental distance  This is the 0th of these quantities
noes.exp-1
the # NOE experimental distance  This is the 1th of these quantities
noes.exp-2
the # NOE experimental distance  This is the 2th of these quantities
noes.score
the Metainference score
noes.neff
effective number of replicas
noes.acceptSigma
MC acceptance for sigma values
noes.sigmaMean-0
uncertainty in the mean estimate  This is the 0th of these quantities
noes.sigma-0
uncertainty parameter  This is the 0th of these quantities
noes.sigmaMean-1
uncertainty in the mean estimate  This is the 1th of these quantities
noes.sigma-1
uncertainty parameter  This is the 1th of these quantities
noes.sigmaMean-2
uncertainty in the mean estimate  This is the 2th of these quantities
noes.sigma-2
uncertainty parameter  This is the 2th of these quantities


PRINT 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=noes.* 
FILE
the name of the file on which to output these quantities 
=colvar The PRINT action with label 

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 labels of the values from which the function is calculated
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...