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| 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 [40] .
The time resolved experiments are read from a text file and intermediate values are obtained by splines.
In the following example a restraint is applied on the time evolution of a saxs spectrum
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 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 ... #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.
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 |
| 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 |
| 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 |
1.8.17