CALIBER

This is part of the isdb module |

Add a time-dependent, harmonic restraint on one or more variables.

This allows implementing a maximum caliber restraint on one or more experimental time series by replica-averaged restrained simulations. See [38] .

The time resolved experiments are read from a text file and intermediate values are obtained by splines.

- Examples

In the following example a restraint is applied on the time evolution of a saxs spectrum

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

MOLINFOSTRUCTURE=first.pdb # Define saxs variablecompulsory keyworda file in pdb format containing a reference structure.saxs:SAXS ...ATOMISTIC( default=off ) calculate SAXS for an atomistic modelATOMS=1-436The atoms to be included in the calculation, e.g.QVALUE1=0.02 # Q-value at which calculate the scatteringSelected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE2=0.0808Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE3=0.1264Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE4=0.1568Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE5=0.172Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE6=0.1872Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE7=0.2176Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE8=0.2328Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE9=0.248Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE10=0.2632Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE11=0.2936Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE12=0.3088Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE13=0.324Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE14=0.3544Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...QVALUE15=0.4 ... #define the caliber restraintSelected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...cal0:CALIBER ...ARG=(saxs\.q_.*)the input for this action is the scalar output from one or more other actions.FILE=expsaxs.datcompulsory keywordthe name of the file containing the time-resolved valuesKAPPA=10compulsory keyworda force constant, this can be use to scale a constant estimated on-the-fly using AVERAGINGSTRIDE=10the frequency with which the forces due to the bias should be calculated.REGRES_ZERO=200stride for regression with zero offsetAVERAGING=200 ...Stride for calculation of the optimum kappa, if 0 only KAPPA is used.

In particular the file expsaxs.dat contains the time traces for the 15 intensities at the selected scattering lengths, organized as time, q_1, etc. The strength of the bias is automatically evaluated from the standard error of the mean over AVERAGING steps and multiplied by KAPPA. This is useful when working with multiple experimental data Because SAXS is usually defined in a manner that is irrespective of a scaling factor the scaling is evaluated from a linear fit every REGRES_ZERO step. Alternatively it can be given as a fixed constant as SCALE. The bias is here applied every tenth step.

- 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 |

bias | the instantaneous value of the bias potential |

x0 | the instantaneous value of the center of the potential |

mean | the current average value of the calculated observable |

kappa | the current force constant |

In addition the following quantities can be calculated by employing the keywords listed below

Quantity | Keyword | Description |

scale | REGRES_ZERO | the current scaling constant |

- Compulsory keywords

FILE | the name of the file containing the time-resolved values |

KAPPA | a force constant, this can be use to scale a constant estimated on-the-fly using AVERAGING |

TSCALE | ( default=1.0 ) Apply a time scaling on the experimental time scale |

SCALE | ( default=1.0 ) Apply a constant scaling on the data provided as arguments |

- Options

NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |

NOENSEMBLE | ( default=off ) don't perform any replica-averaging |

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 the optimum kappa, if 0 only KAPPA is used. |

REGRES_ZERO | stride for regression with zero offset |