PCS

This is part of the isdb module

Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization.

The PCS of an atomic nucleus depends on the \(\theta\) angle between the vector from the spin-label to the nucleus and the external magnetic field and the module of the vector itself [33] . While in principle the averaging resulting from the tumbling should remove the pseudo-contact shift, in presence of the NMR magnetic field the magnetically anisotropic molecule bound to system will break the rotational symmetry does resulting in measurable values for the PCS and RDC.

PCS values can also be calculated using a Single Value Decomposition approach, in this case the code rely on the a set of function from the GNU Scientific Library (GSL). (With SVD forces are not currently implemented).

Replica-Averaged simulations can be performed using PCS values, ENSEMBLE, STATS and RESTRAINT . Metainference simulations can be performed with this CV and METAINFERENCE .

Examples

In the following example five PCS values are defined and their correlation with respect to a set of experimental data is calculated and restrained. In addition, and only for analysis purposes, the same PCS values are calculated using a Single Value Decomposition algorithm.

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

nh: PCS ...
   
ATOMS1
the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. 
=20,21 
   
ATOMS2
the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. 
=20,38 
   
ATOMS3
the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. 
=20,57 
   
ATOMS4
the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. 
=20,77 
   
ATOMS5
the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. 
=20,93 
   
...The PCS action with label nh calculates the following quantities:

 Quantity   
 Description  
nh.rdc-0
the calculated # RDC  This is the 0th of these quantities
nh.rdc-1
the calculated # RDC  This is the 1th of these quantities
nh.rdc-2
the calculated # RDC  This is the 2th of these quantities
nh.rdc-3
the calculated # RDC  This is the 3th of these quantities
nh.rdc-4
the calculated # RDC  This is the 4th of these quantities


enh: ENSEMBLE 
ARG
the input for this action is the scalar output from one or more other actions. 
=nh.* The ENSEMBLE action with label enh calculates the following quantities:

 Quantity   
 Description  
enh.nh.rdc-0
the label of this action is set by user in the input. See documentation above.  This is the 0th of these quantities
enh.nh.rdc-1
the label of this action is set by user in the input. See documentation above.  This is the 1th of these quantities
enh.nh.rdc-2
the label of this action is set by user in the input. See documentation above.  This is the 2th of these quantities
enh.nh.rdc-3
the label of this action is set by user in the input. See documentation above.  This is the 3th of these quantities
enh.nh.rdc-4
the label of this action is set by user in the input. See documentation above.  This is the 4th of these quantities


st: STATS 
ARG
the input for this action is the scalar output from one or more other actions. 
=enh.* 
PARAMETERS
the parameters of the arguments in your function 
=8.17,-8.271,-10.489,-9.871,-9.152 The STATS action with label st calculates the following quantities:

 Quantity   
 Description  
st.sqdevsum
the sum of the squared deviations between arguments and parameters
st.corr
the correlation between arguments and parameters
st.slope
the slope of a linear fit between arguments and parameters
st.intercept
the intercept of a linear fit between arguments and parameters


pcse: RESTRAINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=st.corr 
KAPPA
compulsory keyword ( default=0.0 )
specifies that the restraint is harmonic and what the values of the force constants
on each of the variables are 
=0. 
SLOPE
compulsory keyword ( default=0.0 )
specifies that the restraint is linear and what the values of the force constants
on each of the variables are 
=-25000.0 
AT
compulsory keyword 
the position of the restraint 
=1. The RESTRAINT action with label pcse calculates the following quantities:

 Quantity   
 Description  
pcse.bias
the instantaneous value of the bias potential
pcse.force2
the instantaneous value of the squared force due to this bias potential


PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=st.corr,pcse.bias 
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
rdc	the calculated # RDC

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	SVD/COUPLING	the experimental # RDC
Sxx	SVD	Tensor component
Syy	SVD	Tensor component
Szz	SVD	Tensor component
Sxy	SVD	Tensor component
Sxz	SVD	Tensor component
Syz	SVD	Tensor component

The atoms involved can be specified using

ATOMS

the couple of atoms involved in each of the bonds for which you wish to calculate the RDC. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one dipolar coupling will be calculated for each ATOMS keyword you specify. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3...

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
GYROM	( default=1. ) Add the product of the gyromagnetic constants for the bond.
SCALE	( default=1. ) Add the scaling factor to take into account concentration and other effects.

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
SVD	( default=off ) Set to TRUE if you want to back calculate using Single Value Decomposition (need GSL at compilation time).
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)
COUPLING	Add an experimental value for each coupling (needed by SVD and useful for STATS). You can use multiple instances of this keyword i.e. COUPLING1, COUPLING2, COUPLING3...