Action: NOE

Module	isdb
Description	Usage
Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms

Details and examples

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

NOECalculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms This action has hidden defaults. More details ...
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 activate metainference
SIGMA_MEAN0starting value for the uncertainty in the mean estimate=1
LABELa label for the action so that its output can be referenced in the input to other actions=noesThe NOE action with label noes calculates the following quantities:
 Quantity   
 Type   
 Description  
noes.noe-0
scalar
the # NOE  This is the 0th of these quantities
noes.noe-1
scalar
the # NOE  This is the 1th of these quantities
noes.noe-2
scalar
the # NOE  This is the 2th of these quantities
noes.exp-0
scalar
the # NOE experimental distance  This is the 0th of these quantities
noes.exp-1
scalar
the # NOE experimental distance  This is the 1th of these quantities
noes.exp-2
scalar
the # NOE experimental distance  This is the 2th of these quantities
noes.score
scalar
the Metainference score
noes.neff
scalar
effective number of replicas
noes.acceptSigma
scalar
MC acceptance for sigma values
noes.sigmaMean-0
scalar
uncertainty in the mean estimate  This is the 0th of these quantities
noes.sigma-0
scalar
uncertainty parameter  This is the 0th of these quantities
noes.sigmaMean-1
scalar
uncertainty in the mean estimate  This is the 1th of these quantities
noes.sigma-1
scalar
uncertainty parameter  This is the 1th of these quantities
noes.sigmaMean-2
scalar
uncertainty in the mean estimate  This is the 2th of these quantities
noes.sigma-2
scalar
uncertainty parameter  This is the 2th of these quantities
... NOE
NOECalculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms This action uses the defaults shown here. More details ...
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 activate metainference
SIGMA_MEAN0starting value for the uncertainty in the mean estimate=1
LABELa label for the action so that its output can be referenced in the input to other actions=noes
 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=NONE SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.0 SIGMA_MAX maximum value of the uncertainty parameter=10.
... NOE

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=noes.* FILEthe name of the file on which to output these quantities=colvar

Input

The arguments and atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	scalar	the labels of the values from which the function is calculated
GROUPA	atoms	the atoms involved in each of the contacts you wish to calculate
GROUPB	atoms	the atoms involved in each of the contacts you wish to calculate

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Keyword	Description
score	scalar	default	the Metainference score
sigma	scalar	default	uncertainty parameter
sigmaMean	scalar	default	uncertainty in the mean estimate
neff	scalar	default	effective number of replicas
acceptSigma	scalar	default	MC acceptance for sigma values
acceptScale	scalar	SCALEDATA	MC acceptance for scale value
acceptFT	scalar	GENERIC	MC acceptance for general metainference f tilde value
weight	scalar	REWEIGHT	weights of the weighted average
biasDer	scalar	REWEIGHT	derivatives with respect to the bias
scale	scalar	SCALEDATA	scale parameter
offset	scalar	ADDOFFSET	offset parameter
ftilde	scalar	GENERIC	ensemble average estimator
noe	scalar	default	the # NOE
exp	scalar	NOEDIST	the # NOE experimental distance

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARGThis keyword do not have examples	input	none	the labels of the values from which the function is calculated
GROUPA	input	none	the atoms involved in each of the contacts you wish to calculate
GROUPB	input	none	the atoms involved in each of the contacts you wish to calculate
NOISETYPE	compulsory	MGAUSS	functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
LIKELIHOODThis keyword do not have examples	compulsory	GAUSS	the likelihood for the GENERIC metainference model, GAUSS or LOGN
DFTILDEThis keyword do not have examples	compulsory	0.1	fraction of sigma_mean used to evolve ftilde
SCALE0This keyword do not have examples	compulsory	1.0	initial value of the scaling factor
SCALE_PRIORThis keyword do not have examples	compulsory	FLAT	either FLAT or GAUSSIAN
OFFSET0This keyword do not have examples	compulsory	0.0	initial value of the offset
OFFSET_PRIORThis keyword do not have examples	compulsory	FLAT	either FLAT or GAUSSIAN
SIGMA0	compulsory	1.0	initial value of the uncertainty parameter
SIGMA_MIN	compulsory	0.0	minimum value of the uncertainty parameter
SIGMA_MAX	compulsory	10.	maximum value of the uncertainty parameter
OPTSIGMAMEAN	compulsory	NONE	Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
WRITE_STRIDE	compulsory	10000	write the status to a file every N steps, this can be used for restart/continuation
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
DOSCORE	optional	false	activate metainference
NOENSEMBLEThis keyword do not have examples	optional	false	don't perform any replica-averaging
REWEIGHTThis keyword do not have examples	optional	false	simple REWEIGHT using the ARG as energy
AVERAGINGThis keyword do not have examples	optional	not used	Stride for calculation of averaged weights and sigma_mean
SCALEDATAThis keyword do not have examples	optional	false	Set to TRUE if you want to sample a scaling factor common to all values and replicas
SCALE_MINThis keyword do not have examples	optional	not used	minimum value of the scaling factor
SCALE_MAXThis keyword do not have examples	optional	not used	maximum value of the scaling factor
DSCALEThis keyword do not have examples	optional	not used	maximum MC move of the scaling factor
ADDOFFSETThis keyword do not have examples	optional	false	Set to TRUE if you want to sample an offset common to all values and replicas
OFFSET_MINThis keyword do not have examples	optional	not used	minimum value of the offset
OFFSET_MAXThis keyword do not have examples	optional	not used	maximum value of the offset
DOFFSETThis keyword do not have examples	optional	not used	maximum MC move of the offset
REGRES_ZEROThis keyword do not have examples	optional	not used	stride for regression with zero offset
DSIGMAThis keyword do not have examples	optional	not used	maximum MC move of the uncertainty parameter
SIGMA_MEAN0	optional	not used	starting value for the uncertainty in the mean estimate
SIGMA_MAX_STEPSThis keyword do not have examples	optional	not used	Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used
TEMPThis keyword do not have examples	optional	not used	the system temperature - this is only needed if code doesn't pass the temperature to plumed
MC_STEPSThis keyword do not have examples	optional	not used	number of MC steps
MC_CHUNKSIZEThis keyword do not have examples	optional	not used	MC chunksize
STATUS_FILEThis keyword do not have examples	optional	not used	write a file with all the data useful for restart/continuation of Metainference
FMTThis keyword do not have examples	optional	not used	specify format for HILLS files (useful for decrease the number of digits in regtests)
SELECTORThis keyword do not have examples	optional	not used	name of selector
NSELECTThis keyword do not have examples	optional	not used	range of values for selector [0, N-1]
RESTARTThis keyword do not have examples	optional	not used	allows per-action setting of restart (YES/NO/AUTO)
NOPBCThis keyword do not have examples	optional	false	ignore the periodic boundary conditions when calculating distances
NOEDIST	optional	not used	Add an experimental value for each NOE