PLUMED-NEST

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. 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
        #GPU
        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
        #SOLVATION_STRIDE=
        #SASA_CUTOFF=

#QVALUE RANGE 0.01-0.25 (stride: 0.0150014)

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

# METAINFERENCE
The SAXS action with label saxsdata calculates the following quantities:
 Quantity   
 Description  
saxsdata.score
the Metainference score
saxsdata.sigma
uncertainty parameter
saxsdata.sigmaMean
uncertainty in the mean estimate
saxsdata.neff
effective number of replicas
saxsdata.acceptSigma
MC acceptance for sigma values
saxsdata.acceptScale
MC acceptance for scale value
saxsdata.scale
scale parameter
saxsdata.q
The # SAXS of qsaxsbias: 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
The BIASVALUE action with label saxsbias calculates the following quantities:
 Quantity   
 Description  
saxsbias.bias
the instantaneous value of the bias potential
saxsbias._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileens: 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-.*)

# STATISTICS
The ENSEMBLE action with label ens calculates the following quantities:
 Quantity   
 Description  
ens..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsstatcg: 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-.*)

# PRINT
The STATS action with label statcg calculates the following quantities:
 Quantity   
 Description  
statcg.sqdevsum
the sum of the squared deviations between arguments and parameters
statcg.corr
the correlation between arguments and parameters
statcg.slope
the slope of a linear fit between arguments and parameters
statcg.intercept
the intercept of a linear fit between arguments and parametersPRINTPrint 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