PLUMED-NEST

Project ID: plumID:23.029
Source: GELSOLIN/SLC_ON/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

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=template_AA.pdb

The MOLINFO action with label  calculates something
SAXS
Calculates SAXS intensity. More details
 ...

        
LABEL
a label for the action so that its output can be referenced in the input to other actions
=saxsdata
        
ATOMS
The 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)
=0.080
        
SOLVATION_STRIDE
 Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only)
=100
        
SASA_CUTOFF
 SASA value to consider a residue as exposed to the solvent (ONEBEAD only)
=0.7

#QVALUE RANGE 0.01-0.25 (stride: 0.0150014)

QVALUE1
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.0101007       
EXPINT1
Add an experimental value for each q value
=0.9655268182607186
QVALUE2
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.0251021       
EXPINT2
Add an experimental value for each q value
=0.8074336052768617
QVALUE3
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.0401035       
EXPINT3
Add an experimental value for each q value
=0.5867844124283979
QVALUE4
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.0551049       
EXPINT4
Add an experimental value for each q value
=0.3778068043742405
QVALUE5
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.0701063       
EXPINT5
Add an experimental value for each q value
=0.2199053983683388
QVALUE6
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.0851077       
EXPINT6
Add an experimental value for each q value
=0.1176236764450616
QVALUE7
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1001091       
EXPINT7
Add an experimental value for each q value
=0.0598961117861482
QVALUE8
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1151105       
EXPINT8
Add an experimental value for each q value
=0.0320698663426488
QVALUE9
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1301119       
EXPINT9
Add an experimental value for each q value
=0.0197961291442457
QVALUE10
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1451133      
EXPINT10
Add an experimental value for each q value
=0.0131910258635653
QVALUE11
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1601147      
EXPINT11
Add an experimental value for each q value
=0.0090075507724353
QVALUE12
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1751161      
EXPINT12
Add an experimental value for each q value
=0.0070054764797778
QVALUE13
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1901175      
EXPINT13
Add an experimental value for each q value
=0.0060413990626627
QVALUE14
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.2051189      
EXPINT14
Add an experimental value for each q value
=0.0049136955389689
QVALUE15
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.2201203      
EXPINT15
Add an experimental value for each q value
=0.0039878840479083
QVALUE16
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.2351217      
EXPINT16
Add an experimental value for each q value
=0.0037107186252386
QVALUE17
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.2501231      
EXPINT17
Add 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_STEPS
Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used
=500000
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=500
DOSCORE
 activate metainference
 
SIGMA_MEAN0
starting 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
DSCALE
maximum 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: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(saxsdata\.score 
STRIDE
the 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: 
ENSEMBLE
Calculates the replica averaging of a collective variable over multiple replicas. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(saxsdata\.q

# STATISTICS
The ENSEMBLE action with label ens calculates the following quantities:
 Quantity   
 Description  
ens.value
something calculated by ENSEMBLEstatcg: 
STATS
Calculates statistical properties of a set of collective variables with respect to a set of reference values. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(ens 
PARARG
the 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 parameters
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(ens 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=../ENS.SAXSINT
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(saxsdata\.score),(saxsdata\.scale),(saxsdata\.acceptSigma),(saxsdata\.sigma 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=BAYES.SAXS
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(saxsdata\.q 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=SAXSINT
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=statcg 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=ST.SAXSCG