PLUMED-NEST

Project ID: plumID:23.029
Source: UP1_RNA/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 somethingprotein: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-3124
The GROUP action with label protein calculates somethingrna: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=3125-3511
The GROUP action with label rna calculates something
WRAPAROUND
Rebuild periodic boundary conditions around chosen atoms. More details
 
ATOMS
wrapped atoms
=rna 
AROUND
reference atoms
=protein

#### RESTRAINTS ON CENTER OF RINGS ####
cPHE20: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@CG-20
the CG atom in residue 20. Click here for more information. 
,
@CD1-20
the CD1 atom in residue 20. Click here for more information. 
,
@CE1-20
the CE1 atom in residue 20. Click here for more information. 
,
@CZ-20
the CZ atom in residue 20. Click here for more information. 
,
@CE2-20
the CE2 atom in residue 20. Click here for more information. 
,
@CD2-20
the CD2 atom in residue 20. Click here for more information. 
The CENTER action with label cPHE20 calculates somethingcPHE62: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@CG-62
the CG atom in residue 62. Click here for more information. 
,
@CD1-62
the CD1 atom in residue 62. Click here for more information. 
,
@CE1-62
the CE1 atom in residue 62. Click here for more information. 
,
@CZ-62
the CZ atom in residue 62. Click here for more information. 
,
@CE2-62
the CE2 atom in residue 62. Click here for more information. 
,
@CD2-62
the CD2 atom in residue 62. Click here for more information. 
The CENTER action with label cPHE62 calculates somethingcPHE111: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@CG-111
the CG atom in residue 111. Click here for more information. 
,
@CD1-111
the CD1 atom in residue 111. Click here for more information. 
,
@CE1-111
the CE1 atom in residue 111. Click here for more information. 
,
@CZ-111
the CZ atom in residue 111. Click here for more information. 
,
@CE2-111
the CE2 atom in residue 111. Click here for more information. 
,
@CD2-111
the CD2 atom in residue 111. Click here for more information. 
The CENTER action with label cPHE111 calculates somethingcPHE153: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@CG-153
the CG atom in residue 153. Click here for more information. 
,
@CD1-153
the CD1 atom in residue 153. Click here for more information. 
,
@CE1-153
the CE1 atom in residue 153. Click here for more information. 
,
@CZ-153
the CZ atom in residue 153. Click here for more information. 
,
@CE2-153
the CE2 atom in residue 153. Click here for more information. 
,
@CD2-153
the CD2 atom in residue 153. Click here for more information. 
The CENTER action with label cPHE153 calculates somethingcA4: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@N1-203
the N1 atom in residue 203. Click here for more information. 
,
@C2-203
the C2 atom in residue 203. Click here for more information. 
,
@N3-203
the N3 atom in residue 203. Click here for more information. 
,
@C4-203
the C4 atom in residue 203. Click here for more information. 
,
@C5-203
the C5 atom in residue 203. Click here for more information. 
,
@C6-203
the C6 atom in residue 203. Click here for more information. 
,
@N7-203
the N7 atom in residue 203. Click here for more information. 
,
@C8-203
the C8 atom in residue 203. Click here for more information. 
,
@N9-203
the N9 atom in residue 203. Click here for more information. 
The CENTER action with label cA4 calculates somethingcG5: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@N1-204
the N1 atom in residue 204. Click here for more information. 
,
@C2-204
the C2 atom in residue 204. Click here for more information. 
,
@N3-204
the N3 atom in residue 204. Click here for more information. 
,
@C4-204
the C4 atom in residue 204. Click here for more information. 
,
@C5-204
the C5 atom in residue 204. Click here for more information. 
,
@C6-204
the C6 atom in residue 204. Click here for more information. 
,
@N7-204
the N7 atom in residue 204. Click here for more information. 
,
@C8-204
the C8 atom in residue 204. Click here for more information. 
,
@N9-204
the N9 atom in residue 204. Click here for more information. 
The CENTER action with label cG5 calculates somethingcA9: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@N1-208
the N1 atom in residue 208. Click here for more information. 
,
@C2-208
the C2 atom in residue 208. Click here for more information. 
,
@N3-208
the N3 atom in residue 208. Click here for more information. 
,
@C4-208
the C4 atom in residue 208. Click here for more information. 
,
@C5-208
the C5 atom in residue 208. Click here for more information. 
,
@C6-208
the C6 atom in residue 208. Click here for more information. 
,
@N7-208
the N7 atom in residue 208. Click here for more information. 
,
@C8-208
the C8 atom in residue 208. Click here for more information. 
,
@N9-208
the N9 atom in residue 208. Click here for more information. 
The CENTER action with label cA9 calculates somethingcG10: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@N1-209
the N1 atom in residue 209. Click here for more information. 
,
@C2-209
the C2 atom in residue 209. Click here for more information. 
,
@N3-209
the N3 atom in residue 209. Click here for more information. 
,
@C4-209
the C4 atom in residue 209. Click here for more information. 
,
@C5-209
the C5 atom in residue 209. Click here for more information. 
,
@C6-209
the C6 atom in residue 209. Click here for more information. 
,
@N7-209
the N7 atom in residue 209. Click here for more information. 
,
@C8-209
the C8 atom in residue 209. Click here for more information. 
,
@N9-209
the N9 atom in residue 209. Click here for more information. 
The CENTER action with label cG10 calculates somethingring1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=cPHE20,cA4
The DISTANCE action with label ring1 calculates the following quantities:
 Quantity   
 Description  
ring1.value
the DISTANCE between this pair of atomsring2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=cPHE62,cG5
The DISTANCE action with label ring2 calculates the following quantities:
 Quantity   
 Description  
ring2.value
the DISTANCE between this pair of atomsring3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=cPHE111,cA9
The DISTANCE action with label ring3 calculates the following quantities:
 Quantity   
 Description  
ring3.value
the DISTANCE between this pair of atomsring4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=cPHE153,cG10
The DISTANCE action with label ring4 calculates the following quantities:
 Quantity   
 Description  
ring4.value
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=ring1,ring2,ring3,ring4 
AT
the positions of the wall
=0.35,0.35,0.35,0.35 
KAPPA
the force constant for the wall
=1000.0,1000.0,1000.0,1000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_ring

#### RESTRAINTS ON SALT BRIDGES ####
The UPPER_WALLS action with label uwall_ring calculates somethingsb1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CZ-78
the CZ atom in residue 78. Click here for more information. 
,
@CG-158
the CG atom in residue 158. Click here for more information. 
The DISTANCE action with label sb1 calculates the following quantities:
 Quantity   
 Description  
sb1.value
the DISTANCE between this pair of atomssb2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CZ-91
the CZ atom in residue 91. Click here for more information. 
,
@CG-160
the CG atom in residue 160. Click here for more information. 
The DISTANCE action with label sb2 calculates the following quantities:
 Quantity   
 Description  
sb2.value
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=sb1,sb2 
AT
the positions of the wall
=0.4,0.4 
KAPPA
the force constant for the wall
=1000.0,1000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_sb

#### RESTRAINTS ON SS ####
The UPPER_WALLS action with label uwall_sb calculates somethinga1: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha1.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a1 calculates somethinga2: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha2.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a2 calculates somethinga3: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha3.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a3 calculates somethinga4: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha4.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a4 calculates somethinga5: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha5.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a5 calculates somethinga6: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha6.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a6 calculates somethinga7: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha7.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a7 calculates somethinga8: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha8.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a8 calculates somethinga9: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=alpha9.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label a9 calculates somethingb1: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=beta1.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label b1 calculates somethingb2: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=beta2.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label b2 calculates somethingb3: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=beta3.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label b3 calculates somethingb4: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=beta4.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
The RMSD action with label b4 calculates something
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=a1,a2,a3,a4,a5,a6,a7,a8,a9,b1,b2,b3,b4 
AT
the positions of the wall
=0,0,0,0,0,0,0,0,0,0,0,0,0  
KAPPA
the force constant for the wall
=10000.0,10000.0,10000.0,10000.0,10000.0,20000.0,10000.0,10000.0,10000.0,10000.0,20000.0,10000.0,10000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_ss

#### SAXS ####
The UPPER_WALLS action with label uwall_ss 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
=1-3511
        
ONEBEAD
 calculate SAXS for a single bead model
        
TEMPLATE
 A PDB file is required for ONEBEAD mapping
=template_AA.pdb
	#GPU
	#DEVICEID=0
        
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)
=0.120
        
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)
=0.8
        
SCALE_EXPINT
 Scaling value for experimental data normalization
=0.201148E+01
        
QVALUE1
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.839003E-02	
EXPINT1
Add an experimental value for each q value
=0.198653E+01
QVALUE2
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.167801E-01	
EXPINT2
Add an experimental value for each q value
=0.191350E+01
QVALUE3
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.251701E-01	
EXPINT3
Add an experimental value for each q value
=0.179763E+01
QVALUE4
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.337520E-01    
EXPINT4
Add an experimental value for each q value
=0.164327E+01
QVALUE5
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.423340E-01    
EXPINT5
Add an experimental value for each q value
=0.146336E+01
QVALUE6
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.509160E-01    
EXPINT6
Add an experimental value for each q value
=0.126966E+01
QVALUE7
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.594979E-01    
EXPINT7
Add an experimental value for each q value
=0.107369E+01
QVALUE8
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.680799E-01    
EXPINT8
Add an experimental value for each q value
=0.885614E+00
QVALUE9
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.766619E-01    
EXPINT9
Add an experimental value for each q value
=0.713508E+00
QVALUE10
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.852438E-01   
EXPINT10
Add an experimental value for each q value
=0.562829E+00
QVALUE11
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.938258E-01   
EXPINT11
Add an experimental value for each q value
=0.436336E+00
QVALUE12
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.102408E+00   
EXPINT12
Add an experimental value for each q value
=0.334334E+00
QVALUE13
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.110990E+00   
EXPINT13
Add an experimental value for each q value
=0.255154E+00
QVALUE14
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.119572E+00   
EXPINT14
Add an experimental value for each q value
=0.195774E+00
QVALUE15
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.128154E+00   
EXPINT15
Add an experimental value for each q value
=0.152481E+00
QVALUE16
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.136736E+00   
EXPINT16
Add an experimental value for each q value
=0.121461E+00
QVALUE17
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.145318E+00   
EXPINT17
Add an experimental value for each q value
=0.992440E-01
QVALUE18
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.153900E+00   
EXPINT18
Add an experimental value for each q value
=0.829832E-01
QVALUE19
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.162482E+00   
EXPINT19
Add an experimental value for each q value
=0.705616E-01
QVALUE20
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.171064E+00   
EXPINT20
Add an experimental value for each q value
=0.605595E-01
QVALUE21
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.179645E+00   
EXPINT21
Add an experimental value for each q value
=0.521321E-01
QVALUE22
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.188227E+00   
EXPINT22
Add an experimental value for each q value
=0.448387E-01
QVALUE23
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.196809E+00   
EXPINT23
Add an experimental value for each q value
=0.384860E-01
QVALUE24
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.205391E+00   
EXPINT24
Add an experimental value for each q value
=0.329934E-01
QVALUE25
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.213973E+00   
EXPINT25
Add an experimental value for each q value
=0.283112E-01
QVALUE26
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.222555E+00   
EXPINT26
Add an experimental value for each q value
=0.243814E-01
QVALUE27
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.231137E+00   
EXPINT27
Add an experimental value for each q value
=0.211332E-01
QVALUE28
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.239719E+00   
EXPINT28
Add an experimental value for each q value
=0.184941E-01
QVALUE29
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.248301E+00   
EXPINT29
Add an experimental value for each q value
=0.164044E-01
QVALUE30
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.256883E+00   
EXPINT30
Add an experimental value for each q value
=0.148225E-01
QVALUE31
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.265465E+00   
EXPINT31
Add an experimental value for each q value
=0.137188E-01
QVALUE32
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.274047E+00   
EXPINT32
Add an experimental value for each q value
=0.130615E-01
QVALUE33
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.282629E+00   
EXPINT33
Add an experimental value for each q value
=0.128002E-01
QVALUE34
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.291211E+00   
EXPINT34
Add an experimental value for each q value
=0.128542E-01
QVALUE35
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.299793E+00   
EXPINT35
Add an experimental value for each q value
=0.131114E-01

	# METAINFERENCE
	
DOSCORE
 activate metainference
	
NOENSEMBLE
 don't perform any replica-averaging
	
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0
	
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MGAUSS
	
SCALEDATA
 Set to TRUE if you want to sample a scaling factor common to all values and replicas
 
SCALE_PRIOR
 either FLAT or GAUSSIAN
=GAUSSIAN 
SCALE0
 initial value of the scaling factor
=1.00 
DSCALE
maximum MC move of the scaling factor
=0.001 

        
SIGMA0
 initial value of the uncertainty parameter
=0.1
        
SIGMA_MAX
 maximum value of the uncertainty parameter
=0.1
        
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.00001
        
DSIGMA
maximum MC move of the uncertainty parameter
=0.0005

        
MC_STEPS
number of MC steps
=35 
MC_CHUNKSIZE
MC chunksize
=1
	
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=1000

... 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
=1

# STATISTICS
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 filestatcg: 
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
=(saxsdata\.q 
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
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
ARG
the input for this action is the scalar output from one or more other actions
=ring1,ring2,ring3,ring4,sb1,sb2 
FILE
the name of the file on which to output these quantities
=DISTANCES
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
ARG
the input for this action is the scalar output from one or more other actions
=a1,a2,a3,a4,a5,a6,a7,a8,a9,b1,b2,b3,b4 
FILE
the name of the file on which to output these quantities
=RMSDSS
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
ARG
the input for this action is the scalar output from one or more other actions
=uwall_ring.bias,uwall_sb.bias,uwall_ss.bias 
FILE
the name of the file on which to output these quantities
=RESTRAINTS
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
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\.acceptScale),(saxsdata\.acceptSigma),(saxsdata\.sigma 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=BAYES.SAXS