PLUMED-NEST

Project ID: plumID:21.014
Source: PLUMED-NEST_chignolin/Part2_MM/plumed_PB4_prior.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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../template.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-1the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-2the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-3the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-4the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-5the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-6the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-7the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-8the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-9the 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-10the protein/dna/rna backbone atoms in residue 10. Click here for more information.  NOPBC ignore the periodic boundary conditions when calculating distances

ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
LABELa 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
REFERENCEthe reference values for each of the torsional angles=0
ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information.     COEFFICIENT1the coefficient for each of the torsional angles=-0.01427455
ATOMS2the atoms involved for each of the torsions you wish to calculate=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.     COEFFICIENT2the coefficient for each of the torsional angles=-0.03003557
ATOMS3the atoms involved for each of the torsions you wish to calculate=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.     COEFFICIENT3the coefficient for each of the torsional angles=-0.23777775
ATOMS4the atoms involved for each of the torsions you wish to calculate=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.     COEFFICIENT4the coefficient for each of the torsional angles=0.139227
ATOMS5the atoms involved for each of the torsions you wish to calculate=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.     COEFFICIENT5the coefficient for each of the torsional angles=0.26525215
ATOMS6the atoms involved for each of the torsions you wish to calculate=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.     COEFFICIENT6the coefficient for each of the torsional angles=-0.18108167
ATOMS7the atoms involved for each of the torsions you wish to calculate=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.     COEFFICIENT7the coefficient for each of the torsional angles=0.01530576
ATOMS8the atoms involved for each of the torsions you wish to calculate=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.     COEFFICIENT8the coefficient for each of the torsional angles=0.07231603
ATOMS9the atoms involved for each of the torsions you wish to calculate=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.     COEFFICIENT9the coefficient for each of the torsional angles=-0.1183752
ATOMS10the atoms involved for each of the torsions you wish to calculate=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.   COEFFICIENT10the coefficient for each of the torsional angles=0.00089293
ATOMS11the atoms involved for each of the torsions you wish to calculate=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.   COEFFICIENT11the coefficient for each of the torsional angles=-0.23744683
ATOMS12the atoms involved for each of the torsions you wish to calculate=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information.   COEFFICIENT12the coefficient for each of the torsional angles=0.15661255
ATOMS13the atoms involved for each of the torsions you wish to calculate=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.   COEFFICIENT13the coefficient for each of the torsional angles=0.63855605
ATOMS14the atoms involved for each of the torsions you wish to calculate=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information.   COEFFICIENT14the coefficient for each of the torsional angles=-0.15161411
ATOMS15the atoms involved for each of the torsions you wish to calculate=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.   COEFFICIENT15the coefficient for each of the torsional angles=0.50759965
ATOMS16the atoms involved for each of the torsions you wish to calculate=@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information.   COEFFICIENT16the coefficient for each of the torsional angles=-0.04886669
ATOMS17the atoms involved for each of the torsions you wish to calculate=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.   COEFFICIENT17the coefficient for each of the torsional angles=0.13599118
ATOMS18the atoms involved for each of the torsions you wish to calculate=@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information.  COEFFICIENT18the 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: TORSIONCalculate one or multiple torsional angles. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the four atoms involved in the torsional angle=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@psi-3the 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: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe 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: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe 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: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=back_torsions,back_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=back_comb,back_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif 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: SUMCalculate the sum of the arguments More details ARGthe values input to this function=back_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
back_torsions: TORSIONCalculate one or multiple torsional angles. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the four atoms involved in the torsional angle=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@psi-3the 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: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe 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: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe 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: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=back_torsions,back_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
back_cos: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=back_comb,back_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
back: SUMCalculate the sum of the arguments More details ARGthe values input to this function=back_cos PERIODICif 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 sum of all the switching function on all the distances: CONTACTMAPCalculate 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
SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.6}
ATOMS1the atoms involved in each of the contacts you wish to calculate=s1,s4     WEIGHT1A weight value for a given contact, by default is 1=0.02521988
ATOMS2the atoms involved in each of the contacts you wish to calculate=s1,s5     WEIGHT2A weight value for a given contact, by default is 1=0.20455216
ATOMS3the atoms involved in each of the contacts you wish to calculate=s1,s6     WEIGHT3A weight value for a given contact, by default is 1=-0.54414755
ATOMS4the atoms involved in each of the contacts you wish to calculate=s1,s7     WEIGHT4A weight value for a given contact, by default is 1=0.36219968
ATOMS5the atoms involved in each of the contacts you wish to calculate=s1,s8     WEIGHT5A weight value for a given contact, by default is 1=0.1279484
ATOMS6the atoms involved in each of the contacts you wish to calculate=s1,s9     WEIGHT6A weight value for a given contact, by default is 1=-0.22453008
ATOMS7the atoms involved in each of the contacts you wish to calculate=s1,s10    WEIGHT7A weight value for a given contact, by default is 1=0.29550159
ATOMS8the atoms involved in each of the contacts you wish to calculate=s2,s5     WEIGHT8A weight value for a given contact, by default is 1=-0.03385588
ATOMS9the atoms involved in each of the contacts you wish to calculate=s2,s6     WEIGHT9A weight value for a given contact, by default is 1=0.09919236
ATOMS10the atoms involved in each of the contacts you wish to calculate=s2,s7   WEIGHT10A weight value for a given contact, by default is 1=-0.03330457
ATOMS11the atoms involved in each of the contacts you wish to calculate=s2,s8   WEIGHT11A weight value for a given contact, by default is 1=-0.13847136
ATOMS12the atoms involved in each of the contacts you wish to calculate=s2,s9   WEIGHT12A weight value for a given contact, by default is 1=0.39094173
ATOMS13the atoms involved in each of the contacts you wish to calculate=s2,s10  WEIGHT13A weight value for a given contact, by default is 1=-0.1983029
ATOMS14the atoms involved in each of the contacts you wish to calculate=s3,s6   WEIGHT14A weight value for a given contact, by default is 1=-0.02328201
ATOMS15the atoms involved in each of the contacts you wish to calculate=s3,s7   WEIGHT15A weight value for a given contact, by default is 1=0.0069981
ATOMS16the atoms involved in each of the contacts you wish to calculate=s3,s8   WEIGHT16A weight value for a given contact, by default is 1=0.2231250
ATOMS17the atoms involved in each of the contacts you wish to calculate=s3,s9   WEIGHT17A weight value for a given contact, by default is 1=-0.25618473
ATOMS18the atoms involved in each of the contacts you wish to calculate=s3,s10  WEIGHT18A weight value for a given contact, by default is 1=0.113674
ATOMS19the atoms involved in each of the contacts you wish to calculate=s4,s7   WEIGHT19A weight value for a given contact, by default is 1=0.01257499
ATOMS20the atoms involved in each of the contacts you wish to calculate=s4,s8   WEIGHT20A weight value for a given contact, by default is 1=-0.01498744
ATOMS21the atoms involved in each of the contacts you wish to calculate=s4,s9   WEIGHT21A weight value for a given contact, by default is 1=-0.11663488
ATOMS22the atoms involved in each of the contacts you wish to calculate=s4,s10  WEIGHT22A weight value for a given contact, by default is 1=0.084924
ATOMS23the atoms involved in each of the contacts you wish to calculate=s5,s8   WEIGHT23A weight value for a given contact, by default is 1=-0.005496
ATOMS24the atoms involved in each of the contacts you wish to calculate=s5,s9   WEIGHT24A weight value for a given contact, by default is 1=0.03150733
ATOMS25the atoms involved in each of the contacts you wish to calculate=s5,s10  WEIGHT25A weight value for a given contact, by default is 1=-0.03456732
ATOMS26the atoms involved in each of the contacts you wish to calculate=s6,s9   WEIGHT26A weight value for a given contact, by default is 1=0.00233215
ATOMS27the atoms involved in each of the contacts you wish to calculate=s6,s10  WEIGHT27A weight value for a given contact, by default is 1=0.01574143
ATOMS28the atoms involved in each of the contacts you wish to calculate=s7,s10  WEIGHT28A 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: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@N-1the N atom in residue 1. Click here for more information. ,@CA-1the CA atom in residue 1. Click here for more information. ,@C-1the C atom in residue 1. Click here for more information. ,@N-2the N atom in residue 2. Click here for more information. ,@CA-2the CA atom in residue 2. Click here for more information. ,@C-2the C atom in residue 2. Click here for more information. ,@N-3the N atom in residue 3. Click here for more information. ,@CA-3the CA atom in residue 3. Click here for more information. ,@C-3the C atom in residue 3. Click here for more information. ,@N-4the N atom in residue 4. Click here for more information. ,@CA-4the CA atom in residue 4. Click here for more information. ,@C-4the C atom in residue 4. Click here for more information. ,@N-5the N atom in residue 5. Click here for more information. ,@CA-5the CA atom in residue 5. Click here for more information. ,@C-5the C atom in residue 5. Click here for more information. ,@N-6the N atom in residue 6. Click here for more information. ,@CA-6the CA atom in residue 6. Click here for more information. ,@C-6the C atom in residue 6. Click here for more information. ,@N-7the N atom in residue 7. Click here for more information. ,@CA-7the CA atom in residue 7. Click here for more information. ,@C-7the C atom in residue 7. Click here for more information. ,@N-8the N atom in residue 8. Click here for more information. ,@CA-8the CA atom in residue 8. Click here for more information. ,@C-8the C atom in residue 8. Click here for more information. ,@N-9the N atom in residue 9. Click here for more information. ,@CA-9the CA atom in residue 9. Click here for more information. ,@C-9the C atom in residue 9. Click here for more information. ,@N-10the N atom in residue 10. Click here for more information. ,@CA-10the CA atom in residue 10. Click here for more information. ,@C-10the 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
if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis 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_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf 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: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis 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_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf 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
a vector containing the rmsd distance between each of the residue segments and the reference structure: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis 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_CUTOFFIf 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 SEGMENT1this 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 SEGMENT2this 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 SEGMENT3this 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 SEGMENT4this 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 SEGMENT5this 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 STRUCTURE1the 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_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=hh_rmsd SWITCHThis 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: SUMCalculate the sum of the arguments More details ARGthe values input to this function=hh_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
mmThe PBMETAD action with label mm calculates the following quantities:
 Quantity   
 Type   
 Description  
mm.bias
scalar
the instantaneous value of the bias potential: PBMETADUsed to performed Parallel Bias metadynamics. More details ... 
ARGthe labels of the scalars on which the bias will act=back,cmap,rg,hh 
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.2,0.2,0.2,0.2 
SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.01,0.001,0.004,0.02 
SIGMAthe widths of the Gaussian hills=0.015 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=GEOM 
GRID_MINthe lower bounds for the grid=-4,-2,0.3,0 
GRID_MAXthe upper bounds for the grid=4,2,1.4,3
HEIGHTthe height of the Gaussian hills, one for all biases=0.5 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=10 PACEthe 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 
FILEfiles 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_WFILESdump 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_WSTRIDEfrequency for dumping the grid=10000
...

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=back,cmap,rg,hh,mm.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1000