PLUMED-NEST

Project ID: plumID:21.014
Source: PLUMED-NEST_chignolin/Part1_MetaD_PBMetaD/plumed_ME2.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

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

s1The CENTER_FAST action with label s1 calculates the following quantities:
 Quantity   
 Type   
 Description  
s1
atoms
virtual atom calculated by CENTER_FAST action: 
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
 
s2The CENTER_FAST action with label s2 calculates the following quantities:
 Quantity   
 Type   
 Description  
s2
atoms
virtual atom calculated by CENTER_FAST action: 
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
s3The CENTER_FAST action with label s3 calculates the following quantities:
 Quantity   
 Type   
 Description  
s3
atoms
virtual atom calculated by CENTER_FAST action: 
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
s4The CENTER_FAST action with label s4 calculates the following quantities:
 Quantity   
 Type   
 Description  
s4
atoms
virtual atom calculated by CENTER_FAST action: 
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
s5The CENTER_FAST action with label s5 calculates the following quantities:
 Quantity   
 Type   
 Description  
s5
atoms
virtual atom calculated by CENTER_FAST action: 
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
s6The CENTER_FAST action with label s6 calculates the following quantities:
 Quantity   
 Type   
 Description  
s6
atoms
virtual atom calculated by CENTER_FAST action: 
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
s7The CENTER_FAST action with label s7 calculates the following quantities:
 Quantity   
 Type   
 Description  
s7
atoms
virtual atom calculated by CENTER_FAST action: 
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
s8The CENTER_FAST action with label s8 calculates the following quantities:
 Quantity   
 Type   
 Description  
s8
atoms
virtual atom calculated by CENTER_FAST action: 
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
s9The CENTER_FAST action with label s9 calculates the following quantities:
 Quantity   
 Type   
 Description  
s9
atoms
virtual atom calculated by CENTER_FAST action: 
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
s10The CENTER_FAST action with label s10 calculates the following quantities:
 Quantity   
 Type   
 Description  
s10
atoms
virtual atom calculated by CENTER_FAST action: 
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 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
=backThe ALPHABETA action with label back calculates the following quantities:
 Quantity   
 Type   
 Description  
back
scalar
the alpha beta CV
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):
back_torsionsThe TORSION action with label back_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
back_torsions
vector
the TORSION for each set of specified atoms: 
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_refThe CONSTANT action with label back_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
back_ref
vector
the constant value that was read from the plumed input: 
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_coeffThe CONSTANT action with label back_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
back_coeff
vector
the constant value that was read from the plumed input: 
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_combThe COMBINE action with label back_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
back_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: 
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_cosThe CUSTOM action with label back_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
back_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
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 
backThe SUM action with label back calculates the following quantities:
 Quantity   
 Type   
 Description  
back
scalar
the sum of all the elements in the input vector: 
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 ---           
cmapThe CONTACTMAP action with label cmap calculates the following quantities:
 Quantity   
 Type   
 Description  
cmap
scalar
the value calculated by this action: 
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
...

rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration: 
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
hhThe ANTIBETARMSD action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
scalar
the value calculated by this action: 
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
hh: 
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_rmsdThe SECONDARY_STRUCTURE_RMSD action with label hh_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_rmsd
vector
the value calculated by this action: 
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, 
hh_ltThe LESS_THAN action with label hh_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_lt
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: 
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} 
hhThe SUM action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
scalar
the sum of all the elements in the input vector: 
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 --- 
mmThe METAD action with label mm calculates the following quantities:
 Quantity   
 Type   
 Description  
mm.bias
scalar
the instantaneous value of the bias potential: 
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
=10000000
...

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,mm.bias 
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
=1000