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Action: PCS

Module isdb
Description Usage
Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization. used in 0 tutorialsused in 0 eggs

Details and examples

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 angle between the vector from the spin-label to the nucleus and the external magnetic field and the module of the vector itself the second of the two papers cited below. 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
tested on2.11
PCSCalculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization. This action has hidden defaults. More details ...
ATOMS1the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=20,21
ATOMS2the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=20,38
ATOMS3the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=20,57
ATOMS4the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=20,77
ATOMS5the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=20,93
LABELa label for the action so that its output can be referenced in the input to other actions=nh
... PCS

enh: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=nh.*

st: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=enh.* PARAMETERSthe parameters of the arguments in your function=8.17,-8.271,-10.489,-9.871,-9.152

pcse: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=st.corr KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=0. SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=-25000.0 ATthe position of the restraint=1.

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=st.corr,pcse.bias 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
ATOMS atoms the couple of atoms involved in each of the bonds for which you wish to calculate the RDC

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
rdc scalar default the calculated # RDC
exp scalar SVD/COUPLING the experimental # RDC
Sxx scalar SVD Tensor component
Syy scalar SVD Tensor component
Szz scalar SVD Tensor component
Sxy scalar SVD Tensor component
Sxz scalar SVD Tensor component
Syz scalar SVD Tensor component

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
ATOMS input none the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
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
GYROM compulsory 1. Add the product of the gyromagnetic constants for the bond
SCALE compulsory 1. Add the scaling factor to take into account concentration and other effects
NUMERICAL_DERIVATIVESThis keyword do not have examples optional false calculate the derivatives for these quantities numerically
DOSCOREThis keyword do not have examples 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_MEAN0This keyword do not have examples 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
SVDThis keyword do not have examples optional false Set to TRUE if you want to back calculate using Single Value Decomposition (need GSL at compilation time)
COUPLINGThis keyword do not have examples optional not used Add an experimental value for each coupling (needed by SVD and useful for STATS)

References

More information about how this action can be used is available in the following articles: