PLUMED-NEST-TEST-SITE

Project ID: plumID:21.014
Source: PLUMED-NEST_chignolin/Part2_MM/plumed_ME2_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
The MOLINFO action with label  calculates something
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
 
The CENTER action with label s1 calculates the following quantities:
 Quantity   
 Description  
s1.value
the position of the center of masss2: 
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
The CENTER action with label s2 calculates the following quantities:
 Quantity   
 Description  
s2.value
the position of the center of masss3: 
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
The CENTER action with label s3 calculates the following quantities:
 Quantity   
 Description  
s3.value
the position of the center of masss4: 
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
The CENTER action with label s4 calculates the following quantities:
 Quantity   
 Description  
s4.value
the position of the center of masss5: 
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
The CENTER action with label s5 calculates the following quantities:
 Quantity   
 Description  
s5.value
the position of the center of masss6: 
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
The CENTER action with label s6 calculates the following quantities:
 Quantity   
 Description  
s6.value
the position of the center of masss7: 
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
The CENTER action with label s7 calculates the following quantities:
 Quantity   
 Description  
s7.value
the position of the center of masss8: 
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
The CENTER action with label s8 calculates the following quantities:
 Quantity   
 Description  
s8.value
the position of the center of masss9: 
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
The CENTER action with label s9 calculates the following quantities:
 Quantity   
 Description  
s9.value
the position of the center of masss10: 
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

The CENTER action with label s10 calculates the following quantities:
 Quantity   
 Description  
s10.value
the position of the center of mass
ALPHABETA
Calculate the alpha beta CV This action is a shortcut. 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
...
# PLUMED interprets the command:
# ALPHABETA ...
# NOPBC
# LABEL=back
# REFERENCE=0
# ATOMS1=@psi-1    COEFFICIENT1=-0.01427455
# ATOMS2=@phi-2    COEFFICIENT2=-0.03003557
# ATOMS3=@psi-2    COEFFICIENT3=-0.23777775
# ATOMS4=@phi-3    COEFFICIENT4=0.139227
# ATOMS5=@psi-3    COEFFICIENT5=0.26525215
# ATOMS6=@phi-4    COEFFICIENT6=-0.18108167
# ATOMS7=@psi-4    COEFFICIENT7=0.01530576
# ATOMS8=@phi-5    COEFFICIENT8=0.07231603
# ATOMS9=@psi-5    COEFFICIENT9=-0.1183752
# ATOMS10=@phi-6  COEFFICIENT10=0.00089293
# ATOMS11=@psi-6  COEFFICIENT11=-0.23744683
# ATOMS12=@phi-7  COEFFICIENT12=0.15661255
# ATOMS13=@psi-7  COEFFICIENT13=0.63855605
# ATOMS14=@phi-8  COEFFICIENT14=-0.15161411
# ATOMS15=@psi-8  COEFFICIENT15=0.50759965
# ATOMS16=@phi-9  COEFFICIENT16=-0.04886669
# ATOMS17=@psi-9  COEFFICIENT17=0.13599118
# ATOMS18=@phi-10 COEFFICIENT18=-0.1007816
# ...
# as follows (Click the red comment above to revert to the short version of the input):
The ALPHABETA action with label back calculates the following quantities:
 Quantity   
 Description  
back.value
the alpha beta CVback_torsions: 
TORSION
Calculate a torsional angle. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS1
the four atoms involved in the torsional angle
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
 
ATOMS2
the four atoms involved in the torsional angle
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
 
ATOMS3
the four atoms involved in the torsional angle
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
 
ATOMS4
the four atoms involved in the torsional angle
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
 
ATOMS5
the four atoms involved in the torsional angle
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
     # Action input conctinues with 13 further ATOMSn keywords, 
The TORSION action with label back_torsions calculates the following quantities:
 Quantity   
 Description  
back_torsions.value
the TORSION involving these atomsback_ref: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUES
the numbers that are in your constant value
=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
The CONSTANT action with label back_ref calculates the following quantities:
 Quantity   
 Description  
back_ref.value
the constant value that was read from the plumed inputback_coeff: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUES
the numbers that are in your constant value
=-0.01427455,-0.03003557,-0.23777775,0.139227,0.26525215,-0.18108167,0.01530576,0.07231603,-0.1183752,0.00089293,-0.23744683,0.15661255,0.63855605,-0.15161411,0.50759965,-0.04886669,0.13599118,-0.1007816
The CONSTANT action with label back_coeff calculates the following quantities:
 Quantity   
 Description  
back_coeff.value
the constant value that was read from the plumed inputback_comb: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=back_torsions,back_ref 
COEFFICIENTS
 the coefficients of the arguments in your function
=1,-1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The COMBINE action with label back_comb calculates the following quantities:
 Quantity   
 Description  
back_comb.value
a linear compbinationback_cos: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=back_comb,back_coeff 
FUNC
the function you wish to evaluate
=y*(0.5+0.5*cos(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The CUSTOM action with label back_cos calculates the following quantities:
 Quantity   
 Description  
back_cos.value
an arbitrary functionback: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=back_cos 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
back_torsions: 
TORSION
Calculate a torsional angle. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS1
the four atoms involved in the torsional angle
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
 
ATOMS2
the four atoms involved in the torsional angle
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
 
ATOMS3
the four atoms involved in the torsional angle
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
 
ATOMS4
the four atoms involved in the torsional angle
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
 
ATOMS5
the four atoms involved in the torsional angle
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
     # Action input conctinues with 13 further ATOMSn keywords, 
back_ref: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUES
the numbers that are in your constant value
=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
back_coeff: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUES
the numbers that are in your constant value
=-0.01427455,-0.03003557,-0.23777775,0.139227,0.26525215,-0.18108167,0.01530576,0.07231603,-0.1183752,0.00089293,-0.23744683,0.15661255,0.63855605,-0.15161411,0.50759965,-0.04886669,0.13599118,-0.1007816
back_comb: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=back_torsions,back_ref 
COEFFICIENTS
 the coefficients of the arguments in your function
=1,-1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
back_cos: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=back_comb,back_coeff 
FUNC
the function you wish to evaluate
=y*(0.5+0.5*cos(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
back: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=back_cos 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input ---           
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
The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightshh: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. 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 thresholdhh: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. 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
  
NN
 The n parameter of the switching function
=8 
D_0
 The d_0 parameter of the switching function
=0.0 
MM
 The m parameter of the switching function
=12 
STYLE
 Antiparallel beta sheets can either form in a single chain or from a pair of chains
=all
# PLUMED interprets the command:
# hh: ANTIBETARMSD RESIDUES=all TYPE=DRMSD R_0=0.1 STRANDS_CUTOFF=1 NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
hh_rmsd: 
SECONDARY_STRUCTURE_RMSD
Calclulate the distance between segments of a protein and a reference structure of interest More details
 
BONDLENGTH
the length to use for bonds
=0.17 
ATOMS
this is the full list of atoms that we are investigating
=1,5,7,22,23,24,26,28,43,44,45,47,49,55,56,57,67,64,69,70,71,73,75,84,85,86,88,90,98,99,100,102,104,105,106,107,109,111,119,120,121,123,125,143,144,145,147,149,164,166 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
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
 
SEGMENT1
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 
SEGMENT2
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 
SEGMENT3
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 
SEGMENT4
this is the lists of atoms in the segment that are being considered
=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 
SEGMENT5
this is the lists of atoms in the segment that are being considered
=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 
STRUCTURE1
the reference structure
=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102     # Action input conctinues with 1 further SEGMENTn keywords, 
The SECONDARY_STRUCTURE_RMSD action with label hh_rmsd calculates the following quantities:
 Quantity   
 Description  
hh_rmsd.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
hh_rmsd.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdhh_lt: 
LESS_THAN
Use a switching function to determine how many of the input variables are less than a certain cutoff. More details
 
ARG
the input to this function
=hh_rmsd 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=0.1 D_0=0.0 NN=8 MM=12} 
The LESS_THAN action with label hh_lt calculates the following quantities:
 Quantity   
 Description  
hh_lt.value
a function that is one if the input is less than a thresholdhh: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=hh_lt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
mm: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=cmap,rg
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.2,0.2
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.002,0.004
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.001,0.002
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
=-1,0.3
GRID_MAX
the upper bounds for the grid
=1,1.4
HEIGHT
the heights of the Gaussian hills
=0.5 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
PACE
the frequency for hill addition
=200
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
FILE
 a file in which the list of added hills is stored
=../HILLS
GRID_WFILE
the file on which to write the grid
=../GRID
#GRID_RFILE=../GRID
GRID_WSTRIDE
write the grid to a file every N steps
=100000000
...

The METAD action with label mm calculates the following quantities:
 Quantity   
 Description  
mm.bias
the instantaneous value of the bias potential
SAXS
Calculates SAXS intensity. This action has hidden defaults. 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
=1000000
... 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
SAXS
Calculates SAXS intensity. This action uses the defaults shown here. 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
=1000000
 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10 
DEVICEID
 Identifier of the GPU to be used
=-1 
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)
=0.0 
SOLVATION_STRIDE
 Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only)
=10 
SASA_CUTOFF
 SASA value to consider a residue as exposed to the solvent (ONEBEAD only)
=1.0 
DEUTER_CONC
 Fraction of deuterated solvent
=0 
N
 Number of points in the resolution function integral
=10
... SAXS

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

ens: 
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 the following quantities:
 Quantity   
 Description  
ens..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsst: 
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