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 [27] . 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
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...
1.8.17