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

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 somethingprotein: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1-3124
The GROUP action with label protein calculates somethingrna: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=3125-3511
The GROUP action with label rna calculates somethingWRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=rna AROUNDreference atoms=protein

#### RESTRAINTS ON CENTER OF RINGS ####
cPHE20: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@CG-20the CG atom in residue 20. Click here for more information. ,@CD1-20the CD1 atom in residue 20. Click here for more information. ,@CE1-20the CE1 atom in residue 20. Click here for more information. ,@CZ-20the CZ atom in residue 20. Click here for more information. ,@CE2-20the CE2 atom in residue 20. Click here for more information. ,@CD2-20the CD2 atom in residue 20. Click here for more information. 
The CENTER action with label cPHE20 calculates the following quantities:
 Quantity   
 Description  
cPHE20.value
the position of the center of masscPHE62: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@CG-62the CG atom in residue 62. Click here for more information. ,@CD1-62the CD1 atom in residue 62. Click here for more information. ,@CE1-62the CE1 atom in residue 62. Click here for more information. ,@CZ-62the CZ atom in residue 62. Click here for more information. ,@CE2-62the CE2 atom in residue 62. Click here for more information. ,@CD2-62the CD2 atom in residue 62. Click here for more information. 
The CENTER action with label cPHE62 calculates the following quantities:
 Quantity   
 Description  
cPHE62.value
the position of the center of masscPHE111: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@CG-111the CG atom in residue 111. Click here for more information. ,@CD1-111the CD1 atom in residue 111. Click here for more information. ,@CE1-111the CE1 atom in residue 111. Click here for more information. ,@CZ-111the CZ atom in residue 111. Click here for more information. ,@CE2-111the CE2 atom in residue 111. Click here for more information. ,@CD2-111the CD2 atom in residue 111. Click here for more information. 
The CENTER action with label cPHE111 calculates the following quantities:
 Quantity   
 Description  
cPHE111.value
the position of the center of masscPHE153: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@CG-153the CG atom in residue 153. Click here for more information. ,@CD1-153the CD1 atom in residue 153. Click here for more information. ,@CE1-153the CE1 atom in residue 153. Click here for more information. ,@CZ-153the CZ atom in residue 153. Click here for more information. ,@CE2-153the CE2 atom in residue 153. Click here for more information. ,@CD2-153the CD2 atom in residue 153. Click here for more information. 
The CENTER action with label cPHE153 calculates the following quantities:
 Quantity   
 Description  
cPHE153.value
the position of the center of masscA4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@N1-203the N1 atom in residue 203. Click here for more information. ,@C2-203the C2 atom in residue 203. Click here for more information. ,@N3-203the N3 atom in residue 203. Click here for more information. ,@C4-203the C4 atom in residue 203. Click here for more information. ,@C5-203the C5 atom in residue 203. Click here for more information. ,@C6-203the C6 atom in residue 203. Click here for more information. ,@N7-203the N7 atom in residue 203. Click here for more information. ,@C8-203the C8 atom in residue 203. Click here for more information. ,@N9-203the N9 atom in residue 203. Click here for more information. 
The CENTER action with label cA4 calculates the following quantities:
 Quantity   
 Description  
cA4.value
the position of the center of masscG5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@N1-204the N1 atom in residue 204. Click here for more information. ,@C2-204the C2 atom in residue 204. Click here for more information. ,@N3-204the N3 atom in residue 204. Click here for more information. ,@C4-204the C4 atom in residue 204. Click here for more information. ,@C5-204the C5 atom in residue 204. Click here for more information. ,@C6-204the C6 atom in residue 204. Click here for more information. ,@N7-204the N7 atom in residue 204. Click here for more information. ,@C8-204the C8 atom in residue 204. Click here for more information. ,@N9-204the N9 atom in residue 204. Click here for more information. 
The CENTER action with label cG5 calculates the following quantities:
 Quantity   
 Description  
cG5.value
the position of the center of masscA9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@N1-208the N1 atom in residue 208. Click here for more information. ,@C2-208the C2 atom in residue 208. Click here for more information. ,@N3-208the N3 atom in residue 208. Click here for more information. ,@C4-208the C4 atom in residue 208. Click here for more information. ,@C5-208the C5 atom in residue 208. Click here for more information. ,@C6-208the C6 atom in residue 208. Click here for more information. ,@N7-208the N7 atom in residue 208. Click here for more information. ,@C8-208the C8 atom in residue 208. Click here for more information. ,@N9-208the N9 atom in residue 208. Click here for more information. 
The CENTER action with label cA9 calculates the following quantities:
 Quantity   
 Description  
cA9.value
the position of the center of masscG10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@N1-209the N1 atom in residue 209. Click here for more information. ,@C2-209the C2 atom in residue 209. Click here for more information. ,@N3-209the N3 atom in residue 209. Click here for more information. ,@C4-209the C4 atom in residue 209. Click here for more information. ,@C5-209the C5 atom in residue 209. Click here for more information. ,@C6-209the C6 atom in residue 209. Click here for more information. ,@N7-209the N7 atom in residue 209. Click here for more information. ,@C8-209the C8 atom in residue 209. Click here for more information. ,@N9-209the N9 atom in residue 209. Click here for more information. 
The CENTER action with label cG10 calculates the following quantities:
 Quantity   
 Description  
cG10.value
the position of the center of massring1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe 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: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe 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: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe 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: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe 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 atomsUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=ring1,ring2,ring3,ring4 ATthe positions of the wall=0.35,0.35,0.35,0.35 KAPPAthe force constant for the wall=1000.0,1000.0,1000.0,1000.0 LABELa 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 the following quantities:
 Quantity   
 Description  
uwall_ring.bias
the instantaneous value of the bias potential
uwall_ring.force2
the instantaneous value of the squared force due to this bias potentialsb1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CZ-78the CZ atom in residue 78. Click here for more information. ,@CG-158the 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: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CZ-91the CZ atom in residue 91. Click here for more information. ,@CG-160the 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 atomsUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=sb1,sb2 ATthe positions of the wall=0.4,0.4 KAPPAthe force constant for the wall=1000.0,1000.0 LABELa 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 the following quantities:
 Quantity   
 Description  
uwall_sb.bias
the instantaneous value of the bias potential
uwall_sb.force2
the instantaneous value of the squared force due to this bias potentiala1: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a1.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputa2: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a2.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputa3: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a3.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputa4: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a4.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputa5: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a5.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputa6: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a6.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputa7: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a7.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputa8: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a8.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputa9: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
a9.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputb1: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
b1.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputb2: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
b2.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputb3: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
b3.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputb4: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa 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 the following quantities:
 Quantity   
 Description  
b4.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a1,a2,a3,a4,a5,a6,a7,a8,a9,b1,b2,b3,b4 ATthe positions of the wall=0,0,0,0,0,0,0,0,0,0,0,0,0  KAPPAthe 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 LABELa 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 the following quantities:
 Quantity   
 Description  
uwall_ss.bias
the instantaneous value of the bias potential
uwall_ss.force2
the instantaneous value of the squared force due to this bias potentialSAXSCalculates 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=1-3511
        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
        
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.839003E-02	EXPINT1Add an experimental value for each q value=0.198653E+01
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.167801E-01	EXPINT2Add an experimental value for each q value=0.191350E+01
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.251701E-01	EXPINT3Add an experimental value for each q value=0.179763E+01
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.337520E-01    EXPINT4Add an experimental value for each q value=0.164327E+01
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.423340E-01    EXPINT5Add an experimental value for each q value=0.146336E+01
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.509160E-01    EXPINT6Add an experimental value for each q value=0.126966E+01
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.594979E-01    EXPINT7Add an experimental value for each q value=0.107369E+01
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.680799E-01    EXPINT8Add an experimental value for each q value=0.885614E+00
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.766619E-01    EXPINT9Add an experimental value for each q value=0.713508E+00
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.852438E-01   EXPINT10Add an experimental value for each q value=0.562829E+00
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.938258E-01   EXPINT11Add an experimental value for each q value=0.436336E+00
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.102408E+00   EXPINT12Add an experimental value for each q value=0.334334E+00
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.110990E+00   EXPINT13Add an experimental value for each q value=0.255154E+00
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.119572E+00   EXPINT14Add an experimental value for each q value=0.195774E+00
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.128154E+00   EXPINT15Add an experimental value for each q value=0.152481E+00
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.136736E+00   EXPINT16Add an experimental value for each q value=0.121461E+00
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.145318E+00   EXPINT17Add an experimental value for each q value=0.992440E-01
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.153900E+00   EXPINT18Add an experimental value for each q value=0.829832E-01
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.162482E+00   EXPINT19Add an experimental value for each q value=0.705616E-01
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.171064E+00   EXPINT20Add an experimental value for each q value=0.605595E-01
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.179645E+00   EXPINT21Add an experimental value for each q value=0.521321E-01
QVALUE22Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.188227E+00   EXPINT22Add an experimental value for each q value=0.448387E-01
QVALUE23Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.196809E+00   EXPINT23Add an experimental value for each q value=0.384860E-01
QVALUE24Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.205391E+00   EXPINT24Add an experimental value for each q value=0.329934E-01
QVALUE25Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.213973E+00   EXPINT25Add an experimental value for each q value=0.283112E-01
QVALUE26Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.222555E+00   EXPINT26Add an experimental value for each q value=0.243814E-01
QVALUE27Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.231137E+00   EXPINT27Add an experimental value for each q value=0.211332E-01
QVALUE28Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.239719E+00   EXPINT28Add an experimental value for each q value=0.184941E-01
QVALUE29Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.248301E+00   EXPINT29Add an experimental value for each q value=0.164044E-01
QVALUE30Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.256883E+00   EXPINT30Add an experimental value for each q value=0.148225E-01
QVALUE31Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.265465E+00   EXPINT31Add an experimental value for each q value=0.137188E-01
QVALUE32Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.274047E+00   EXPINT32Add an experimental value for each q value=0.130615E-01
QVALUE33Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.282629E+00   EXPINT33Add an experimental value for each q value=0.128002E-01
QVALUE34Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.291211E+00   EXPINT34Add an experimental value for each q value=0.128542E-01
QVALUE35Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.299793E+00   EXPINT35Add an experimental value for each q value=0.131114E-01

	# METAINFERENCE
	DOSCORE activate metainference
	NOENSEMBLE don't perform any replica-averaging
	SIGMA_MEAN0starting 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 DSCALEmaximum 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
        DSIGMAmaximum MC move of the uncertainty parameter=0.0005

        MC_STEPSnumber of MC steps=35 MC_CHUNKSIZEMC 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: 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=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: 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=(saxsdata\.q-.*) 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 STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=ring1,ring2,ring3,ring4,sb1,sb2 FILEthe name of the file on which to output these quantities=DISTANCES
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=a1,a2,a3,a4,a5,a6,a7,a8,a9,b1,b2,b3,b4 FILEthe name of the file on which to output these quantities=RMSDSS
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=uwall_ring.bias,uwall_sb.bias,uwall_ss.bias FILEthe name of the file on which to output these quantities=RESTRAINTS
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
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\.acceptScale),(saxsdata\.acceptSigma),(saxsdata\.sigma.*) STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=BAYES.SAXS