Action: CALIBER

Module	isdb
Description	Usage
Add a time-dependent, harmonic restraint on one or more variables.

Details and examples

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.

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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=first.pdb

# Define saxs variable
The MOLINFO action with label  calculates somethingSAXSCalculates SAXS intensity. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=saxs
ATOMISTIC Calculate SAXS for an atomistic model
ATOMSThe atoms to be included in the calculation, e=1-436
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.02 # Q-value at which calculate the scattering
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0808
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1264
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1568
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.172
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1872
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2176
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2328
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.248
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2632
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2936
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.3088
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.324
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.3544
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.4
... SAXS


#define the caliber restraint
The SAXS action with label saxs calculates the following quantities:
 Quantity   
 Description  
saxs.score
the Metainference score
saxs.sigma
uncertainty parameter
saxs.sigmaMean
uncertainty in the mean estimate
saxs.neff
effective number of replicas
saxs.acceptSigma
MC acceptance for sigma values
saxs.q
The # SAXS of qCALIBERAdd a time-dependent, harmonic restraint on one or more variables. More details ...
  ARGthe labels of the scalars on which the bias will act=(saxs\.q_.*)
  FILEthe name of the file containing the time-resolved values=expsaxs.dat
  KAPPAa force constant, this can be use to scale a constant estimated on-the-fly using AVERAGING=10
  LABELa label for the action so that its output can be referenced in the input to other actions=cal0
  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
... CALIBER
The CALIBER action with label cal0 calculates the following quantities:
 Quantity   
 Description  
cal0.bias
the instantaneous value of the bias potential
cal0.x0
the instantaneous value of the center of the potential
cal0.mean
the current average value of the calculated observable
cal0.kappa
the current force constant
cal0.scale
the current scaling constant

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.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	scalar	the labels of the scalars on which the bias will act

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Keyword	Description
bias	scalar	default	the instantaneous value of the bias potential
x0	scalar	default	the instantaneous value of the center of the potential
mean	scalar	default	the current average value of the calculated observable
kappa	scalar	default	the current force constant
scale	scalar	REGRES_ZERO	the current scaling constant

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the labels of the scalars on which the bias will act
FILE	compulsory	none	the name of the file containing the time-resolved values
KAPPA	compulsory	none	a force constant, this can be use to scale a constant estimated on-the-fly using AVERAGING
TSCALEThis keyword do not have examples	compulsory	1.0	Apply a time scaling on the experimental time scale
SCALEThis keyword do not have examples	compulsory	1.0	Apply a constant scaling on the data provided as arguments
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOENSEMBLEThis keyword do not have examples	optional	false	don't perform any replica-averaging
AVERAGING	optional	not used	Stride for calculation of the optimum kappa, if 0 only KAPPA is used
REGRES_ZERO	optional	not used	stride for regression with zero offset

References

More information about how this action can be used is available in the following articles:

• R. Capelli, G. Tiana, C. Camilloni, An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations. The Journal of Chemical Physics. 148 (2018)