PLUMED-NEST

Project ID: plumID:21.014
Source: PLUMED-NEST_chignolin/Part2_MM/plumed_PB4_MM.dat
Originally used with PLUMED version: 2.7
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

#SETTINGS NREPLICAS=2
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.pdb
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-166

s1: 
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
=
@back-1
the protein/dna/rna backbone atoms in residue 1. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
s2: 
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
=
@back-2
the protein/dna/rna backbone atoms in residue 2. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
s3: 
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
=
@back-3
the protein/dna/rna backbone atoms in residue 3. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
s4: 
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
=
@back-4
the protein/dna/rna backbone atoms in residue 4. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
s5: 
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
=
@back-5
the protein/dna/rna backbone atoms in residue 5. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
s6: 
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
=
@back-6
the protein/dna/rna backbone atoms in residue 6. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
s7: 
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
=
@back-7
the protein/dna/rna backbone atoms in residue 7. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
s8: 
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
=
@back-8
the protein/dna/rna backbone atoms in residue 8. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
s9: 
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
=
@back-9
the protein/dna/rna backbone atoms in residue 9. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
s10: 
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
=
@back-10
the protein/dna/rna backbone atoms in residue 10. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

ALPHABETA
Calculate the alpha beta CV More details
 ...
NOPBC
 ignore the periodic boundary conditions when calculating distances
LABEL
a label for the action so that its output can be referenced in the input to other actions
=back
REFERENCE
the reference values for each of the torsional angles
=0
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
    
COEFFICIENT1
the coefficient for each of the torsional angles
=-0.01427455
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
    
COEFFICIENT2
the coefficient for each of the torsional angles
=-0.03003557
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
    
COEFFICIENT3
the coefficient for each of the torsional angles
=-0.23777775
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
    
COEFFICIENT4
the coefficient for each of the torsional angles
=0.139227
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
    
COEFFICIENT5
the coefficient for each of the torsional angles
=0.26525215
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
    
COEFFICIENT6
the coefficient for each of the torsional angles
=-0.18108167
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
    
COEFFICIENT7
the coefficient for each of the torsional angles
=0.01530576
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
    
COEFFICIENT8
the coefficient for each of the torsional angles
=0.07231603
ATOMS9
the atoms involved for each of the torsions you wish to calculate
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
    
COEFFICIENT9
the coefficient for each of the torsional angles
=-0.1183752
ATOMS10
the atoms involved for each of the torsions you wish to calculate
=
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
  
COEFFICIENT10
the coefficient for each of the torsional angles
=0.00089293
ATOMS11
the atoms involved for each of the torsions you wish to calculate
=
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
  
COEFFICIENT11
the coefficient for each of the torsional angles
=-0.23744683
ATOMS12
the atoms involved for each of the torsions you wish to calculate
=
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
  
COEFFICIENT12
the coefficient for each of the torsional angles
=0.15661255
ATOMS13
the atoms involved for each of the torsions you wish to calculate
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
  
COEFFICIENT13
the coefficient for each of the torsional angles
=0.63855605
ATOMS14
the atoms involved for each of the torsions you wish to calculate
=
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
  
COEFFICIENT14
the coefficient for each of the torsional angles
=-0.15161411
ATOMS15
the atoms involved for each of the torsions you wish to calculate
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
  
COEFFICIENT15
the coefficient for each of the torsional angles
=0.50759965
ATOMS16
the atoms involved for each of the torsions you wish to calculate
=
@phi-9
the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. 
  
COEFFICIENT16
the coefficient for each of the torsional angles
=-0.04886669
ATOMS17
the atoms involved for each of the torsions you wish to calculate
=
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
  
COEFFICIENT17
the coefficient for each of the torsional angles
=0.13599118
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@phi-10
the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. 
 
COEFFICIENT18
the coefficient for each of the torsional angles
=-0.1007816
...
          
cmap: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 ...
NOPBC
 ignore the periodic boundary conditions when calculating distances
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.6}
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=s1,s4     
WEIGHT1
A weight value for a given contact, by default is 1
=0.02521988
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=s1,s5     
WEIGHT2
A weight value for a given contact, by default is 1
=0.20455216
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=s1,s6     
WEIGHT3
A weight value for a given contact, by default is 1
=-0.54414755
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=s1,s7     
WEIGHT4
A weight value for a given contact, by default is 1
=0.36219968
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=s1,s8     
WEIGHT5
A weight value for a given contact, by default is 1
=0.1279484
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=s1,s9     
WEIGHT6
A weight value for a given contact, by default is 1
=-0.22453008
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=s1,s10    
WEIGHT7
A weight value for a given contact, by default is 1
=0.29550159
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=s2,s5     
WEIGHT8
A weight value for a given contact, by default is 1
=-0.03385588
ATOMS9
the atoms involved in each of the contacts you wish to calculate
=s2,s6     
WEIGHT9
A weight value for a given contact, by default is 1
=0.09919236
ATOMS10
the atoms involved in each of the contacts you wish to calculate
=s2,s7   
WEIGHT10
A weight value for a given contact, by default is 1
=-0.03330457
ATOMS11
the atoms involved in each of the contacts you wish to calculate
=s2,s8   
WEIGHT11
A weight value for a given contact, by default is 1
=-0.13847136
ATOMS12
the atoms involved in each of the contacts you wish to calculate
=s2,s9   
WEIGHT12
A weight value for a given contact, by default is 1
=0.39094173
ATOMS13
the atoms involved in each of the contacts you wish to calculate
=s2,s10  
WEIGHT13
A weight value for a given contact, by default is 1
=-0.1983029
ATOMS14
the atoms involved in each of the contacts you wish to calculate
=s3,s6   
WEIGHT14
A weight value for a given contact, by default is 1
=-0.02328201
ATOMS15
the atoms involved in each of the contacts you wish to calculate
=s3,s7   
WEIGHT15
A weight value for a given contact, by default is 1
=0.0069981
ATOMS16
the atoms involved in each of the contacts you wish to calculate
=s3,s8   
WEIGHT16
A weight value for a given contact, by default is 1
=0.2231250
ATOMS17
the atoms involved in each of the contacts you wish to calculate
=s3,s9   
WEIGHT17
A weight value for a given contact, by default is 1
=-0.25618473
ATOMS18
the atoms involved in each of the contacts you wish to calculate
=s3,s10  
WEIGHT18
A weight value for a given contact, by default is 1
=0.113674
ATOMS19
the atoms involved in each of the contacts you wish to calculate
=s4,s7   
WEIGHT19
A weight value for a given contact, by default is 1
=0.01257499
ATOMS20
the atoms involved in each of the contacts you wish to calculate
=s4,s8   
WEIGHT20
A weight value for a given contact, by default is 1
=-0.01498744
ATOMS21
the atoms involved in each of the contacts you wish to calculate
=s4,s9   
WEIGHT21
A weight value for a given contact, by default is 1
=-0.11663488
ATOMS22
the atoms involved in each of the contacts you wish to calculate
=s4,s10  
WEIGHT22
A weight value for a given contact, by default is 1
=0.084924
ATOMS23
the atoms involved in each of the contacts you wish to calculate
=s5,s8   
WEIGHT23
A weight value for a given contact, by default is 1
=-0.005496
ATOMS24
the atoms involved in each of the contacts you wish to calculate
=s5,s9   
WEIGHT24
A weight value for a given contact, by default is 1
=0.03150733
ATOMS25
the atoms involved in each of the contacts you wish to calculate
=s5,s10  
WEIGHT25
A weight value for a given contact, by default is 1
=-0.03456732
ATOMS26
the atoms involved in each of the contacts you wish to calculate
=s6,s9   
WEIGHT26
A weight value for a given contact, by default is 1
=0.00233215
ATOMS27
the atoms involved in each of the contacts you wish to calculate
=s6,s10  
WEIGHT27
A weight value for a given contact, by default is 1
=0.01574143
ATOMS28
the atoms involved in each of the contacts you wish to calculate
=s7,s10  
WEIGHT28
A weight value for a given contact, by default is 1
=-0.01026257
SUM
 calculate the sum of all the contacts in the input
...

The CONTACTMAP action with label cmap calculates the following quantities:
 Quantity   
 Description  
cmap.contact
By not using SUM or CMDIST each contact will be stored in a componentrg: 
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@N-1
the N atom in residue 1. Click here for more information. 
,
@CA-1
the CA atom in residue 1. Click here for more information. 
,
@C-1
the C atom in residue 1. Click here for more information. 
,
@N-2
the N atom in residue 2. Click here for more information. 
,
@CA-2
the CA atom in residue 2. Click here for more information. 
,
@C-2
the C atom in residue 2. Click here for more information. 
,
@N-3
the N atom in residue 3. Click here for more information. 
,
@CA-3
the CA atom in residue 3. Click here for more information. 
,
@C-3
the C atom in residue 3. Click here for more information. 
,
@N-4
the N atom in residue 4. Click here for more information. 
,
@CA-4
the CA atom in residue 4. Click here for more information. 
,
@C-4
the C atom in residue 4. Click here for more information. 
,
@N-5
the N atom in residue 5. Click here for more information. 
,
@CA-5
the CA atom in residue 5. Click here for more information. 
,
@C-5
the C atom in residue 5. Click here for more information. 
,
@N-6
the N atom in residue 6. Click here for more information. 
,
@CA-6
the CA atom in residue 6. Click here for more information. 
,
@C-6
the C atom in residue 6. Click here for more information. 
,
@N-7
the N atom in residue 7. Click here for more information. 
,
@CA-7
the CA atom in residue 7. Click here for more information. 
,
@C-7
the C atom in residue 7. Click here for more information. 
,
@N-8
the N atom in residue 8. Click here for more information. 
,
@CA-8
the CA atom in residue 8. Click here for more information. 
,
@C-8
the C atom in residue 8. Click here for more information. 
,
@N-9
the N atom in residue 9. Click here for more information. 
,
@CA-9
the CA atom in residue 9. Click here for more information. 
,
@C-9
the C atom in residue 9. Click here for more information. 
,
@N-10
the N atom in residue 10. Click here for more information. 
,
@CA-10
the CA atom in residue 10. Click here for more information. 
,
@C-10
the C atom in residue 10. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
hh: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=all 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
R_0
The r_0 parameter of the switching function
=0.1 
STRANDS_CUTOFF
If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like
=1 
NOPBC
 ignore the periodic boundary conditions

The ANTIBETARMSD action with label hh calculates the following quantities:
 Quantity   
 Description  
hh.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
hh.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdmm: 
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ... 
ARG
the input for this action is the scalar output from one or more other actions
=back,cmap,rg,hh 
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.2,0.2,0.2,0.2 
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.01,0.001,0.004,0.02 
SIGMA
the widths of the Gaussian hills
=0.015 
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=GEOM 
GRID_MIN
the lower bounds for the grid
=-4,-2,0.3,0 
GRID_MAX
the upper bounds for the grid
=4,2,1.4,3
HEIGHT
the height of the Gaussian hills, one for all biases
=0.5 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=10 
PACE
the frequency for hill addition, one for all biases
=200 
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
 
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=../HILLS.back,../HILLS.cmap,../HILLS.rg,../HILLS.hh
GRID_WFILES
dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES
=../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hh
#GRID_RFILES=../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hh
GRID_WSTRIDE
frequency for dumping the grid
=10000000
...

The PBMETAD action with label mm calculates the following quantities:
 Quantity   
 Description  
mm.bias
the instantaneous value of the bias potential
SAXS
Calculates SAXS intensity. More details
 ...
        
NOPBC
 Ignore the periodic boundary conditions when calculating distances
        #GPU
        
LABEL
a label for the action so that its output can be referenced in the input to other actions
=saxs
        
ATOMS
The atoms to be included in the calculation, e
=1-166  
        
ATOMISTIC
 Calculate SAXS for an atomistic model
        
SCALE_EXPINT
 Scaling value for experimental data normalization
=100

	
QVALUE1
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.010000	
EXPINT1
Add an experimental value for each q value
=99.884787
	
QVALUE2
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.070000	
EXPINT2
Add an experimental value for each q value
=94.573283
	
QVALUE3
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.130000	
EXPINT3
Add an experimental value for each q value
=82.964898
	
QVALUE4
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.190000	
EXPINT4
Add an experimental value for each q value
=68.296624
	
QVALUE5
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.250000	
EXPINT5
Add an experimental value for each q value
=53.565198
	
QVALUE6
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.310000	
EXPINT6
Add an experimental value for each q value
=40.540191
	
QVALUE7
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.370000	
EXPINT7
Add an experimental value for each q value
=29.869842
	
QVALUE8
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.430000	
EXPINT8
Add an experimental value for each q value
=21.605034
	
QVALUE9
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.490000	
EXPINT9
Add an experimental value for each q value
=15.542217
	
QVALUE10
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.550000	
EXPINT10
Add an experimental value for each q value
=11.346918
	
QVALUE11
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.610000	
EXPINT11
Add an experimental value for each q value
=8.628281
	
QVALUE12
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.670000	
EXPINT12
Add an experimental value for each q value
=7.008095
	
QVALUE13
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.730000	
EXPINT13
Add an experimental value for each q value
=6.154012
	
QVALUE14
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.790000	
EXPINT14
Add an experimental value for each q value
=5.789840
	
QVALUE15
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.850000	
EXPINT15
Add an experimental value for each q value
=5.711048
	
QVALUE16
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.910000	
EXPINT16
Add an experimental value for each q value
=5.799616
	
QVALUE17
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.970000	
EXPINT17
Add an experimental value for each q value
=6.016059
	
QVALUE18
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=1.030000	
EXPINT18
Add an experimental value for each q value
=6.361548
	
QVALUE19
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=1.090000	
EXPINT19
Add an experimental value for each q value
=6.825863
	
QVALUE20
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=1.150000	
EXPINT20
Add an experimental value for each q value
=7.352355	
	
QVALUE21
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=1.210000	
EXPINT21
Add an experimental value for each q value
=7.844432
	
QVALUE22
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=1.270000	
EXPINT22
Add an experimental value for each q value
=8.208167
	
QVALUE23
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=1.330000	
EXPINT23
Add an experimental value for each q value
=8.399227
	
QVALUE24
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=1.390000	
EXPINT24
Add an experimental value for each q value
=8.442345

        
DOSCORE
 activate metainference
        
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
ARG
the input for this action is the scalar output from one or more other actions
=mm.bias
        
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
=FLAT 
SCALE0
 initial value of the scaling factor
=1.00 
SCALE_MIN
minimum value of the scaling factor
=0.5 
SCALE_MAX
maximum value of the scaling factor
=1.5 
DSCALE
maximum MC move of the scaling factor
=0.0002
        
SIGMA0
 initial value of the uncertainty parameter
=1
        
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.001
        
MC_CHUNKSIZE
MC chunksize
=2 
MC_STEPS
number of MC steps
=12 
        
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=3
        
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM_MAX 
	
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200
        
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000
... SAXS

The SAXS action with label saxs calculates the following quantities:
 Quantity   
 Description  
saxs.score
the Metainference score
saxs.sigma
uncertainty parameter
saxs.sigmaMean
uncertainty in the mean estimate
saxs.neff
effective number of replicas
saxs.acceptSigma
MC acceptance for sigma values
saxs.acceptScale
MC acceptance for scale value
saxs.weight
weights of the weighted average
saxs.biasDer
derivatives with respect to the bias
saxs.scale
scale parameter
saxs.q
The # SAXS of q
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
=saxs.score 
STRIDE
the frequency with which the forces due to the bias should be calculated
=2

The BIASVALUE action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
._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
=(saxs\.q-.*),mm.bias 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
The ENSEMBLE action with label ens calculates a scalar quantityst: 
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\.saxs\.q 
PARARG
the input for this action is the scalar output from one or more other actions without derivatives
=(saxs\.exp

The STATS action with label st calculates the following quantities:
 Quantity   
 Description  
st.sqdevsum
the sum of the squared deviations between arguments and parameters
st.corr
the correlation between arguments and parameters
st.slope
the slope of a linear fit between arguments and parameters
st.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
=(saxs\.score),(saxs\.biasDer),(saxs\.weight),(saxs\.neff),(saxs\.scale),(saxs\.acceptScale),(saxs\.acceptSigma),(saxs\.sigma  
FILE
the name of the file on which to output these quantities
=BAYES 
STRIDE
 the frequency with which the quantities of interest should be output
=5000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=st.*,(ens\.saxs\.q 
FILE
the name of the file on which to output these quantities
=STATS 
STRIDE
 the frequency with which the quantities of interest should be output
=5000
#PRINT ARG=(saxs\.q-.*)  FILE=QVALUE STRIDE=5000

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=back,cmap,rg,hh 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=5000