SAXS

This is part of the isdb module |

Calculates SAXS scattered intensity using either the Debye equation.

Intensities are calculated for a set of scattering length set using QVALUE keywords that are numbered starting from 0. Structure factors can be either assigned using a polynomial expansion to any order using the PARAMETERS keywords; automatically assigned to atoms using the ATOMISTIC flag reading a PDB file, a correction for the water density is automatically added, with water density that by default is 0.334 but that can be set otherwise using WATERDENS; automatically assigned to Martini pseudo atoms using the MARTINI flag. The calculated intensities can be scaled using the SCALEINT keywords. This is applied by rescaling the structure factors. Experimental reference intensities can be added using the EXPINT keywords. By default SAXS is calculated using Debye on CPU, by adding the GPU flag it is possible to solve the equation on a GPU if the ARRAYFIRE libraries are installed and correctly linked. METAINFERENCE can be activated using DOSCORE and the other relevant keywords.

- Examples
- in the following example the saxs intensities for a martini model are calculated. structure factors are obtained from the pdb file indicated in the MOLINFO.

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

MOLINFOPRINT ARG=(saxs\.q-.*),(saxs\.exp-.*) FILE=colvar STRIDE=1STRUCTURE=template.pdbcompulsory keyworda file in pdb format containing a reference structure.saxs:SAXS ...ATOMS=1-355The atoms to be included in the calculation, e.g.SCALEINT=3920000compulsory keyword ( default=1.0 )SCALING value of the calculated data.MARTINI( default=off ) calculate SAXS for a Martini modelQVALUE1=0.02Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT1=1.0902Add an experimental value for each q value.QVALUE2=0.05Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT2=0.790632Add an experimental value for each q value.QVALUE3=0.08Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT3=0.453808Add an experimental value for each q value.QVALUE4=0.11Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT4=0.254737Add an experimental value for each q value.QVALUE5=0.14Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT5=0.154928Add an experimental value for each q value.QVALUE6=0.17Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT6=0.0921503Add an experimental value for each q value.QVALUE7=0.2Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT7=0.052633Add an experimental value for each q value.QVALUE8=0.23Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT8=0.0276557Add an experimental value for each q value.QVALUE9=0.26Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT9=0.0122775Add an experimental value for each q value.QVALUE10=0.29Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT10=0.00880634Add an experimental value for each q value.QVALUE11=0.32Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT11=0.0137301Add an experimental value for each q value.QVALUE12=0.35Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT12=0.0180036Add an experimental value for each q value.QVALUE13=0.38Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT13=0.0193374Add an experimental value for each q value.QVALUE14=0.41Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT14=0.0210131Add an experimental value for each q value.QVALUE15=0.44Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ...EXPINT15=0.0220506 ...Add an experimental value for each q value.

- 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 |

score | the Metainference score |

sigma | uncertainty parameter |

sigmaMean | uncertainty in the mean estimate |

neff | effective number of replicas |

acceptSigma | MC acceptance for sigma values |

q | the # SAXS of q |

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

Quantity | Keyword | Description |

acceptScale | SCALEDATA | MC acceptance for scale value |

acceptFT | GENERIC | MC acceptance for general metainference f tilde value |

weight | REWEIGHT | weights of the weighted average |

biasDer | REWEIGHT | derivatives with respect to the bias |

scale | SCALEDATA | scale parameter |

offset | ADDOFFSET | offset parameter |

ftilde | GENERIC | ensemble average estimator |

exp | EXPINT | the # experimental intensity |

- The atoms involved can be specified using

ATOMS | The atoms to be included in the calculation, e.g. the whole protein.. For more information on how to specify lists of atoms see Groups and Virtual Atoms |

- Compulsory keywords

NOISETYPE | ( default=MGAUSS ) functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC) |

LIKELIHOOD | ( default=GAUSS ) the likelihood for the GENERIC metainference model, GAUSS or LOGN |

DFTILDE | ( default=0.1 ) fraction of sigma_mean used to evolve ftilde |

SCALE0 | ( default=1.0 ) initial value of the scaling factor |

SCALE_PRIOR | ( default=FLAT ) either FLAT or GAUSSIAN |

OFFSET0 | ( default=0.0 ) initial value of the offset |

OFFSET_PRIOR | ( default=FLAT ) either FLAT or GAUSSIAN |

SIGMA0 | ( default=1.0 ) initial value of the uncertainty parameter |

SIGMA_MIN | ( default=0.0 ) minimum value of the uncertainty parameter |

SIGMA_MAX | ( default=10. ) maximum value of the uncertainty parameter |

OPTSIGMAMEAN | ( default=NONE ) Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly |

WRITE_STRIDE | ( default=10000 ) write the status to a file every N steps, this can be used for restart/continuation |

DEVICEID | ( default=0 ) Identifier of the GPU to be used |

WATERDENS | ( default=0.334 ) Density of the water to be used for the correction of atomistic structure factors. |

SCALEINT | ( default=1.0 ) SCALING value of the calculated data. Useful to simplify the comparison. |

- Options

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

DOSCORE | ( default=off ) activate metainference |

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

REWEIGHT | ( default=off ) simple REWEIGHT using the ARG as energy |

SCALEDATA | ( default=off ) Set to TRUE if you want to sample a scaling factor common to all values and replicas |

ADDOFFSET | ( default=off ) Set to TRUE if you want to sample an offset common to all values and replicas |

NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |

SERIAL | ( default=off ) Perform the calculation in serial - for debug purpose |

GPU | ( default=off ) calculate SAXS using ARRAYFIRE on an accelerator device |

ATOMISTIC | ( default=off ) calculate SAXS for an atomistic model |

MARTINI | ( default=off ) calculate SAXS for a Martini model |

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 averaged weights and sigma_mean |

SCALE_MIN | minimum value of the scaling factor |

SCALE_MAX | maximum value of the scaling factor |

DSCALE | maximum MC move of the scaling factor |

OFFSET_MIN | minimum value of the offset |

OFFSET_MAX | maximum value of the offset |

DOFFSET | maximum MC move of the offset |

REGRES_ZERO | stride for regression with zero offset |

DSIGMA | maximum MC move of the uncertainty parameter |

SIGMA_MEAN0 | starting value for the uncertainty in the mean estimate |

SIGMA_MAX_STEPS | Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used |

TEMP | the system temperature - this is only needed if code doesn't pass the temperature to plumed |

MC_STEPS | number of MC steps |

MC_CHUNKSIZE | MC chunksize |

STATUS_FILE | write a file with all the data useful for restart/continuation of Metainference |

SELECTOR | name of selector |

NSELECT | range of values for selector [0, N-1] |

RESTART | allows per-action setting of restart (YES/NO/AUTO) |

QVALUE | Selected scattering lengths in Angstrom are given as QVALUE1, QVALUE2, ... . You can use multiple instances of this keyword i.e. QVALUE1, QVALUE2, QVALUE3... |

PARAMETERS | Used parameter Keywords like PARAMETERS1, PARAMETERS2. These are used to calculate the structure factor for the \(i\)th atom/bead. You can use multiple instances of this keyword i.e. PARAMETERS1, PARAMETERS2, PARAMETERS3... |

EXPINT | Add an experimental value for each q value. You can use multiple instances of this keyword i.e. EXPINT1, EXPINT2, EXPINT3... |