NOE

This is part of the isdb module |

Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms or ambiguous NOE.

Each NOE is defined by two groups containing the same number of atoms, distances are calculated in pairs, transformed in 1/r^6, summed and saved as components.

\[ NOE() = (\frac{1}{N_{eq}}\sum_j^{N_{eq}} (\frac{1}{r_j^6})) \]

NOE can be used to calculate a Metainference score over one or more replicas using the intrinsic implementation of METAINFERENCE that is activated by DOSCORE.

- Examples
- In the following examples three noes are defined, the first is calculated based on the distances of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances 4-15,4-16,8-15,8-16. METAINFERENCE is activated using DOSCORE.

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

noes:NOE ...GROUPA1=1,3the atoms involved in each of the contacts you wish to calculate.GROUPB1=2,2the atoms involved in each of the contacts you wish to calculate.NOEDIST1=0.6Add an experimental value for each NOE.GROUPA2=5the atoms involved in each of the contacts you wish to calculate.GROUPB2=7the atoms involved in each of the contacts you wish to calculate.NOEDIST2=0.6Add an experimental value for each NOE.GROUPA3=4,4,8,8the atoms involved in each of the contacts you wish to calculate.GROUPB3=15,16,15,16the atoms involved in each of the contacts you wish to calculate.NOEDIST3=0.6Add an experimental value for each NOE.DOSCORE( default=off ) activate metainferenceSIGMA_MEAN0=1 ... PRINTcould not find this keywordARG=the input for this action is the scalar output from one or more other actions.noes.*FILE=colvarthe name of the file on which to output these quantities

- 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 |

noe | the # NOE |

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 | NOEDIST | the # NOE experimental distance |

- The atoms involved can be specified using

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... |

GROUPB | the atoms involved in each of the contacts you wish to calculate. Keywords like GROUPB1, GROUPB2, GROUPB3,... 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. GROUPB1, GROUPB2, GROUPB3... |

- 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 |

- 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 |

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) |

NOEDIST | Add an experimental value for each NOE. You can use multiple instances of this keyword i.e. NOEDIST1, NOEDIST2, NOEDIST3... |