Project ID: plumID:23.029
Source: GELSOLIN/SLC_OFF/plumed.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
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=template_AA.pdb
The MOLINFO action with label calculates somethingSAXSCalculates SAXS intensity. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=saxsdataThe SAXS action with label saxsdata calculates the following quantities:| Quantity | Type | Description |
| saxsdata.q-0 | scalar | The # SAXS of q This is the 0th of these quantities |
| saxsdata.q-1 | scalar | The # SAXS of q This is the 1th of these quantities |
| saxsdata.q-2 | scalar | The # SAXS of q This is the 2th of these quantities |
| saxsdata.q-3 | scalar | The # SAXS of q This is the 3th of these quantities |
| saxsdata.q-4 | scalar | The # SAXS of q This is the 4th of these quantities |
| saxsdata.q-5 | scalar | The # SAXS of q This is the 5th of these quantities |
| saxsdata.q-6 | scalar | The # SAXS of q This is the 6th of these quantities |
| saxsdata.q-7 | scalar | The # SAXS of q This is the 7th of these quantities |
| saxsdata.q-8 | scalar | The # SAXS of q This is the 8th of these quantities |
| saxsdata.q-9 | scalar | The # SAXS of q This is the 9th of these quantities |
| saxsdata.q-10 | scalar | The # SAXS of q This is the 10th of these quantities |
| saxsdata.q-11 | scalar | The # SAXS of q This is the 11th of these quantities |
| saxsdata.q-12 | scalar | The # SAXS of q This is the 12th of these quantities |
| saxsdata.q-13 | scalar | The # SAXS of q This is the 13th of these quantities |
| saxsdata.q-14 | scalar | The # SAXS of q This is the 14th of these quantities |
| saxsdata.q-15 | scalar | The # SAXS of q This is the 15th of these quantities |
| saxsdata.q-16 | scalar | The # SAXS of q This is the 16th of these quantities |
| saxsdata.exp-0 | scalar | The # experimental intensity This is the 0th of these quantities |
| saxsdata.exp-1 | scalar | The # experimental intensity This is the 1th of these quantities |
| saxsdata.exp-2 | scalar | The # experimental intensity This is the 2th of these quantities |
| saxsdata.exp-3 | scalar | The # experimental intensity This is the 3th of these quantities |
| saxsdata.exp-4 | scalar | The # experimental intensity This is the 4th of these quantities |
| saxsdata.exp-5 | scalar | The # experimental intensity This is the 5th of these quantities |
| saxsdata.exp-6 | scalar | The # experimental intensity This is the 6th of these quantities |
| saxsdata.exp-7 | scalar | The # experimental intensity This is the 7th of these quantities |
| saxsdata.exp-8 | scalar | The # experimental intensity This is the 8th of these quantities |
| saxsdata.exp-9 | scalar | The # experimental intensity This is the 9th of these quantities |
| saxsdata.exp-10 | scalar | The # experimental intensity This is the 10th of these quantities |
| saxsdata.exp-11 | scalar | The # experimental intensity This is the 11th of these quantities |
| saxsdata.exp-12 | scalar | The # experimental intensity This is the 12th of these quantities |
| saxsdata.exp-13 | scalar | The # experimental intensity This is the 13th of these quantities |
| saxsdata.exp-14 | scalar | The # experimental intensity This is the 14th of these quantities |
| saxsdata.exp-15 | scalar | The # experimental intensity This is the 15th of these quantities |
| saxsdata.exp-16 | scalar | The # experimental intensity This is the 16th of these quantities |
| saxsdata.score | scalar | the Metainference score |
| saxsdata.neff | scalar | effective number of replicas |
| saxsdata.scale | scalar | scale parameter |
| saxsdata.acceptScale | scalar | MC acceptance for scale value |
| saxsdata.acceptSigma | scalar | MC acceptance for sigma values |
| saxsdata.sigmaMean-0 | scalar | uncertainty in the mean estimate This is the 0th of these quantities |
| saxsdata.sigma-0 | scalar | uncertainty parameter This is the 0th of these quantities |
| saxsdata.sigmaMean-1 | scalar | uncertainty in the mean estimate This is the 1th of these quantities |
| saxsdata.sigma-1 | scalar | uncertainty parameter This is the 1th of these quantities |
| saxsdata.sigmaMean-2 | scalar | uncertainty in the mean estimate This is the 2th of these quantities |
| saxsdata.sigma-2 | scalar | uncertainty parameter This is the 2th of these quantities |
| saxsdata.sigmaMean-3 | scalar | uncertainty in the mean estimate This is the 3th of these quantities |
| saxsdata.sigma-3 | scalar | uncertainty parameter This is the 3th of these quantities |
| saxsdata.sigmaMean-4 | scalar | uncertainty in the mean estimate This is the 4th of these quantities |
| saxsdata.sigma-4 | scalar | uncertainty parameter This is the 4th of these quantities |
| saxsdata.sigmaMean-5 | scalar | uncertainty in the mean estimate This is the 5th of these quantities |
| saxsdata.sigma-5 | scalar | uncertainty parameter This is the 5th of these quantities |
| saxsdata.sigmaMean-6 | scalar | uncertainty in the mean estimate This is the 6th of these quantities |
| saxsdata.sigma-6 | scalar | uncertainty parameter This is the 6th of these quantities |
| saxsdata.sigmaMean-7 | scalar | uncertainty in the mean estimate This is the 7th of these quantities |
| saxsdata.sigma-7 | scalar | uncertainty parameter This is the 7th of these quantities |
| saxsdata.sigmaMean-8 | scalar | uncertainty in the mean estimate This is the 8th of these quantities |
| saxsdata.sigma-8 | scalar | uncertainty parameter This is the 8th of these quantities |
| saxsdata.sigmaMean-9 | scalar | uncertainty in the mean estimate This is the 9th of these quantities |
| saxsdata.sigma-9 | scalar | uncertainty parameter This is the 9th of these quantities |
| saxsdata.sigmaMean-10 | scalar | uncertainty in the mean estimate This is the 10th of these quantities |
| saxsdata.sigma-10 | scalar | uncertainty parameter This is the 10th of these quantities |
| saxsdata.sigmaMean-11 | scalar | uncertainty in the mean estimate This is the 11th of these quantities |
| saxsdata.sigma-11 | scalar | uncertainty parameter This is the 11th of these quantities |
| saxsdata.sigmaMean-12 | scalar | uncertainty in the mean estimate This is the 12th of these quantities |
| saxsdata.sigma-12 | scalar | uncertainty parameter This is the 12th of these quantities |
| saxsdata.sigmaMean-13 | scalar | uncertainty in the mean estimate This is the 13th of these quantities |
| saxsdata.sigma-13 | scalar | uncertainty parameter This is the 13th of these quantities |
| saxsdata.sigmaMean-14 | scalar | uncertainty in the mean estimate This is the 14th of these quantities |
| saxsdata.sigma-14 | scalar | uncertainty parameter This is the 14th of these quantities |
| saxsdata.sigmaMean-15 | scalar | uncertainty in the mean estimate This is the 15th of these quantities |
| saxsdata.sigma-15 | scalar | uncertainty parameter This is the 15th of these quantities |
| saxsdata.sigmaMean-16 | scalar | uncertainty in the mean estimate This is the 16th of these quantities |
| saxsdata.sigma-16 | scalar | uncertainty parameter This is the 16th of these quantities |
ATOMSThe atoms to be included in the calculation, e=1-11880
ONEBEAD calculate SAXS for a single bead model
TEMPLATE A PDB file is required for ONEBEAD mapping=template_AA.pdb
SOLVDENS Density of the solvent to be used for the correction of atomistic form factors=0.334
SOLVATION_CORRECTION Solvation layer electron density correction (ONEBEAD only)=0.00
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0101007 EXPINT1Add an experimental value for each q value=0.9655268182607186
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0251021 EXPINT2Add an experimental value for each q value=0.8074336052768617
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0401035 EXPINT3Add an experimental value for each q value=0.5867844124283979
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0551049 EXPINT4Add an experimental value for each q value=0.3778068043742405
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0701063 EXPINT5Add an experimental value for each q value=0.2199053983683388
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0851077 EXPINT6Add an experimental value for each q value=0.1176236764450616
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1001091 EXPINT7Add an experimental value for each q value=0.0598961117861482
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1151105 EXPINT8Add an experimental value for each q value=0.0320698663426488
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1301119 EXPINT9Add an experimental value for each q value=0.0197961291442457
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1451133 EXPINT10Add an experimental value for each q value=0.0131910258635653
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1601147 EXPINT11Add an experimental value for each q value=0.0090075507724353
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1751161 EXPINT12Add an experimental value for each q value=0.0070054764797778
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1901175 EXPINT13Add an experimental value for each q value=0.0060413990626627
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2051189 EXPINT14Add an experimental value for each q value=0.0049136955389689
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2201203 EXPINT15Add an experimental value for each q value=0.0039878840479083
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2351217 EXPINT16Add an experimental value for each q value=0.0037107186252386
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2501231 EXPINT17Add an experimental value for each q value=0.0033106578718972
OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM_MAX
SIGMA_MAX_STEPSNumber of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used=500000
AVERAGINGStride for calculation of averaged weights and sigma_mean=500
DOSCORE activate metainference SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5
SCALEDATA Set to TRUE if you want to sample a scaling factor common to all values and replicas SCALE0 initial value of the scaling factor=1.0
DSCALEmaximum MC move of the scaling factor=0.01 SCALE_PRIOR either FLAT or GAUSSIAN=GAUSSIAN
SIGMA0 initial value of the uncertainty parameter=0.5 SIGMA_MIN minimum value of the uncertainty parameter=0.0001 SIGMA_MAX maximum value of the uncertainty parameter=0.5
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS
... SAXS
SAXSCalculates SAXS intensity. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=saxsdata
ATOMSThe atoms to be included in the calculation, e=1-11880
ONEBEAD calculate SAXS for a single bead model
TEMPLATE A PDB file is required for ONEBEAD mapping=template_AA.pdb
SOLVDENS Density of the solvent to be used for the correction of atomistic form factors=0.334
SOLVATION_CORRECTION Solvation layer electron density correction (ONEBEAD only)=0.00
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0101007 EXPINT1Add an experimental value for each q value=0.9655268182607186
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0251021 EXPINT2Add an experimental value for each q value=0.8074336052768617
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0401035 EXPINT3Add an experimental value for each q value=0.5867844124283979
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0551049 EXPINT4Add an experimental value for each q value=0.3778068043742405
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0701063 EXPINT5Add an experimental value for each q value=0.2199053983683388
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0851077 EXPINT6Add an experimental value for each q value=0.1176236764450616
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1001091 EXPINT7Add an experimental value for each q value=0.0598961117861482
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1151105 EXPINT8Add an experimental value for each q value=0.0320698663426488
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1301119 EXPINT9Add an experimental value for each q value=0.0197961291442457
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1451133 EXPINT10Add an experimental value for each q value=0.0131910258635653
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1601147 EXPINT11Add an experimental value for each q value=0.0090075507724353
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1751161 EXPINT12Add an experimental value for each q value=0.0070054764797778
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1901175 EXPINT13Add an experimental value for each q value=0.0060413990626627
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2051189 EXPINT14Add an experimental value for each q value=0.0049136955389689
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2201203 EXPINT15Add an experimental value for each q value=0.0039878840479083
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2351217 EXPINT16Add an experimental value for each q value=0.0037107186252386
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2501231 EXPINT17Add an experimental value for each q value=0.0033106578718972
OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM_MAX
SIGMA_MAX_STEPSNumber of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used=500000
AVERAGINGStride for calculation of averaged weights and sigma_mean=500
DOSCORE activate metainference SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5
SCALEDATA Set to TRUE if you want to sample a scaling factor common to all values and replicas SCALE0 initial value of the scaling factor=1.0
DSCALEmaximum MC move of the scaling factor=0.01 SCALE_PRIOR either FLAT or GAUSSIAN=GAUSSIAN
SIGMA0 initial value of the uncertainty parameter=0.5 SIGMA_MIN minimum value of the uncertainty parameter=0.0001 SIGMA_MAX maximum value of the uncertainty parameter=0.5
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000 DEVICEID Identifier of the GPU to be used=-1 SCALE_EXPINT Scaling value for experimental data normalization=1.0 SOLVATION_STRIDE Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only)=10 SASA_CUTOFF SASA value to consider a residue as exposed to the solvent (ONEBEAD only)=1.0 DEUTER_CONC Fraction of deuterated solvent=0. N Number of points in the resolution function integral=10
... SAXS
saxsbiasThe BIASVALUE action with label saxsbias calculates the following quantities:| Quantity | Type | Description |
| saxsbias.bias | scalar | the instantaneous value of the bias potential |
| saxsbias.saxsdata.score_bias | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named saxsdata.score |
: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=(saxsdata\.score) STRIDEthe frequency with which the forces due to the bias should be calculated=2
ensThe ENSEMBLE action with label ens calculates the following quantities:| Quantity | Type | Description |
| ens.saxsdata.q-0 | scalar | the average for argument saxsdata.q-0 |
| ens.saxsdata.q-1 | scalar | the average for argument saxsdata.q-1 |
| ens.saxsdata.q-2 | scalar | the average for argument saxsdata.q-2 |
| ens.saxsdata.q-3 | scalar | the average for argument saxsdata.q-3 |
| ens.saxsdata.q-4 | scalar | the average for argument saxsdata.q-4 |
| ens.saxsdata.q-5 | scalar | the average for argument saxsdata.q-5 |
| ens.saxsdata.q-6 | scalar | the average for argument saxsdata.q-6 |
| ens.saxsdata.q-7 | scalar | the average for argument saxsdata.q-7 |
| ens.saxsdata.q-8 | scalar | the average for argument saxsdata.q-8 |
| ens.saxsdata.q-9 | scalar | the average for argument saxsdata.q-9 |
| ens.saxsdata.q-10 | scalar | the average for argument saxsdata.q-10 |
| ens.saxsdata.q-11 | scalar | the average for argument saxsdata.q-11 |
| ens.saxsdata.q-12 | scalar | the average for argument saxsdata.q-12 |
| ens.saxsdata.q-13 | scalar | the average for argument saxsdata.q-13 |
| ens.saxsdata.q-14 | scalar | the average for argument saxsdata.q-14 |
| ens.saxsdata.q-15 | scalar | the average for argument saxsdata.q-15 |
| ens.saxsdata.q-16 | scalar | the average for argument saxsdata.q-16 |
: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(saxsdata\.q-.*)
statcgThe STATS action with label statcg calculates the following quantities:| Quantity | Type | Description |
| statcg.sqdevsum | scalar | the sum of the squared deviations between arguments and parameters |
| statcg.corr | scalar | the correlation between arguments and parameters |
| statcg.slope | scalar | the slope of a linear fit between arguments and parameters |
| statcg.intercept | scalar | the intercept of a linear fit between arguments and parameters |
: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=(ens.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(saxsdata\.exp-.*)
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(ens.*) STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=../ENS.SAXSINT
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxsdata\.score),(saxsdata\.scale),(saxsdata\.acceptSigma),(saxsdata\.sigma.*) STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=BAYES.SAXS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxsdata\.q-.*) STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=SAXSINT
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=statcg.* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=ST.SAXSCG
