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 [31] .

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 
STRUCTURE
compulsory keyword 
a file in pdb format containing a reference structure. 
=first.pdb  You cannot view the components that are calculated by each action for this input file. Sorry 
# Define saxs variable
saxs: SAXS ...
   
   
ATOMISTIC
( default=off ) Calculate SAXS for an atomistic model 
 
   
ATOMS
The atoms to be included in the calculation, e.g. 
=1-436 
   
QVALUE1
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.02 # Q-value at which calculate the scattering 
   
QVALUE2
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.0808 
   
QVALUE3
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.1264 
   
QVALUE4
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.1568 
   
QVALUE5
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.172 
   
QVALUE6
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.1872 
   
QVALUE7
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.2176 
   
QVALUE8
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.2328 
   
QVALUE9
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.248 
   
QVALUE10
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.2632 
   
QVALUE11
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.2936 
   
QVALUE12
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.3088 
   
QVALUE13
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.324 
   
QVALUE14
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.3544 
   
QVALUE15
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ....
=0.4 
... You cannot view the components that are calculated by each action for this input file. Sorry 
#define the caliber restraint
cal0: CALIBER ...
   
ARG
compulsory keyword 
the labels of the scalars on which the bias will act 
=(saxs\.q_.*) 
   
FILE
compulsory keyword 
the name of the file containing the time-resolved values 
=expsaxs.dat 
   
KAPPA
compulsory keyword 
a force constant, this can be use to scale a constant estimated on-the-fly using
AVERAGING 
=10 
   
   
STRIDE
the frequency with which the forces due to the bias should be calculated. 
=10 
   
REGRES_ZERO
stride for regression with zero offset 
=200 
   
AVERAGING
Stride for calculation of the optimum kappa, if 0 only KAPPA is used. 
=200 
... You cannot view the components that are calculated by each action for this input file. Sorry 

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

ARG	the labels of the scalars on which the bias will act
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
AVERAGING	Stride for calculation of the optimum kappa, if 0 only KAPPA is used.
REGRES_ZERO	stride for regression with zero offset