This is part of the isdb module

Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms .

The reference atom for the spin label is added with SPINLABEL, the affected atom(s) are give as numbered GROUPA1, GROUPA2, ... The additional parameters needed for the calculation are given as INEPT, the inept time, TAUC the correlation time, OMEGA, the Larmor frequency and RTWO for the relaxation time.

METAINFERENCE can be activated using DOSCORE and the other relevant keywords.

Examples

In the following example five PRE intensities are calculated using the distance between the oxygen of the spin label and the backbone hydrogen atoms. Omega is the NMR frequency, RTWO the R2 for the hydrogen atoms, INEPT of 8 ms for the experiment and a TAUC of 1.21 ns

Click on the labels of the actions for more information on what each action computes

HN_pre: PRE ...

INEPTcompulsory keyword
is the INEPT time (in ms). =8
TAUCcompulsory keyword
is the correlation time (in ns) for this electron-nuclear interaction. =1.21
OMEGAcompulsory keyword
is the Larmor frequency of the nuclear spin (in MHz). =900
SPINLABELThe atom to be used as the paramagnetic center.. =1818
GROUPA1the atoms involved in each of the contacts you wish to calculate.
=86 RTWO1The relaxation of the atom/atoms in the corresponding GROUPA of atoms. =0.0120272827
GROUPA2the atoms involved in each of the contacts you wish to calculate.
=177 RTWO2The relaxation of the atom/atoms in the corresponding GROUPA of atoms. =0.0263953158
GROUPA3the atoms involved in each of the contacts you wish to calculate.
=285 RTWO3The relaxation of the atom/atoms in the corresponding GROUPA of atoms. =0.0058899829
GROUPA4the atoms involved in each of the contacts you wish to calculate.
=335 RTWO4The relaxation of the atom/atoms in the corresponding GROUPA of atoms. =0.0102072646
GROUPA5the atoms involved in each of the contacts you wish to calculate.
=451 RTWO5The relaxation of the atom/atoms in the corresponding GROUPA of atoms. =0.0086341843
...The PRE action with label HN_pre calculates the following quantities:

Quantity Description
HN_pre.pre-0 the # PRE This is the 0th of these quantities
HN_pre.pre-1 the # PRE This is the 1th of these quantities
HN_pre.pre-2 the # PRE This is the 2th of these quantities
HN_pre.pre-3 the # PRE This is the 3th of these quantities
HN_pre.pre-4 the # PRE This is the 4th of these quantities

PRINT ARG=HN_pre.* FILE=PRE.dat STRIDE=1

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
pre	the # PRE

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	PREINT	the # PRE experimental intensity

The atoms involved can be specified using

SPINLABEL	The atom to be used as the paramagnetic center.. For more information on how to specify lists of atoms see Groups and Virtual Atoms
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...

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
INEPT	is the INEPT time (in ms).
TAUC	is the correlation time (in ns) for this electron-nuclear interaction.
OMEGA	is the Larmor frequency of the nuclear spin (in MHz).

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
NORATIO	( default=off ) Set to TRUE if you want to compute PRE without Intensity Ratio
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)
RTWO	The relaxation of the atom/atoms in the corresponding GROUPA of atoms. Keywords like RTWO1, RTWO2, RTWO3,... should be listed.. You can use multiple instances of this keyword i.e. RTWO1, RTWO2, RTWO3...
PREINT	Add an experimental value for each PRE.. You can use multiple instances of this keyword i.e. PREINT1, PREINT2, PREINT3...

Quantity	Description
HN_pre.pre-0	the # PRE This is the 0th of these quantities
HN_pre.pre-1	the # PRE This is the 1th of these quantities
HN_pre.pre-2	the # PRE This is the 2th of these quantities
HN_pre.pre-3	the # PRE This is the 3th of these quantities
HN_pre.pre-4	the # PRE This is the 4th of these quantities