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 [35] .

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
MOLINFO STRUCTUREcompulsory keyword
a file in pdb format containing a reference structure. =first.pdb
# Define saxs variable
saxs: SAXS ...

ATOMISTIC( default=off ) calculate SAXS for an atomistic model
ATOMSThe atoms to be included in the calculation, e.g. =1-436
QVALUE1Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.02 # Q-value at which calculate the scattering
QVALUE2Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.0808
QVALUE3Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.1264
QVALUE4Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.1568
QVALUE5Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.172
QVALUE6Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.1872
QVALUE7Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.2176
QVALUE8Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.2328
QVALUE9Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.248
QVALUE10Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.2632
QVALUE11Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.2936
QVALUE12Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.3088
QVALUE13Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.324
QVALUE14Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.3544
QVALUE15Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... =0.4
...
#define the caliber restraint
cal0: CALIBER ...
ARGthe input for this action is the scalar output from one or more other actions. =(saxs\.q_.*)
FILEcompulsory keyword
the name of the file containing the time-resolved values =expsaxs.dat
KAPPAcompulsory keyword
a force constant, this can be use to scale a constant estimated on-the-fly using
AVERAGING =10

STRIDEthe frequency with which the forces due to the bias should be calculated. =10
REGRES_ZEROstride for regression with zero offset =200
AVERAGINGStride for calculation of the optimum kappa, if 0 only KAPPA is used. =200
...


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