| 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 ...
=8
=1.21
=900
=1818
=86 =0.0120272827
=177 =0.0263953158
=285 =0.0058899829
=335 =0.0102072646
=451 =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 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) |
| 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... |
1.8.17