Action: PRE
| Module | isdb |
|---|---|
| Description | Usage |
| Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms . |   |
Details and examples
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
PRECalculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms . This action has hidden defaults. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=HN_pre INEPTis the INEPT time (in ms)=8 TAUCis the correlation time (in ns) for this electron-nuclear interaction=1.21 OMEGAis 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 ... PRE
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=HN_pre.* FILEthe name of the file on which to output these quantities=PRE.dat STRIDE the frequency with which the quantities of interest should be output=1
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 |
| SPINLABEL | atoms | The atom to be used as the paramagnetic center |
| GROUPA | 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 |
| pre | scalar | default | the # PRE |
| exp | scalar | PREINT | the # PRE experimental intensity |
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 |
| SPINLABEL | input | none | The atom to be used as the paramagnetic center |
| GROUPA | 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 |
| INEPT | compulsory | none | is the INEPT time (in ms) |
| TAUC | compulsory | none | is the correlation time (in ns) for this electron-nuclear interaction |
| OMEGA | compulsory | none | is the Larmor frequency of the nuclear spin (in MHz) |
| 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 |
| NORATIOThis keyword do not have examples | optional | false | Set to TRUE if you want to compute PRE without Intensity Ratio |
| RTWO | optional | not used | The relaxation of the atom/atoms in the corresponding GROUPA of atoms |
| PREINTThis keyword do not have examples | optional | not used | Add an experimental value for each PRE |