PLUMED-NEST

Project ID: plumID:20.020
Source: plumed_cv.dat
Originally used with PLUMED version: 2.2
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

# protein info
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=trp.pdb

# whole molecule for all the backbone atoms
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details RESIDUESthis command specifies that the backbone atoms in a set of residues all must be aligned=all MOLTYPEthe type of molecule that is under study=protein

# CA-radius of gyration
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=5,19,38,59,78,95,119,138,160,172,179,194,200,211,222,229,261,275,289,295 NOPBC ignore the periodic boundary conditions when calculating distances

# number of backbone hydrogen bonds
COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details ...
# 19 backbone oxygen atoms
GROUPAFirst list of atoms=16,35,56,75,92,116,135,157,169,176,183,197,208,219,226,250,264,278,292 
# 15 backbone hydrogen atoms
GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=18,37,58,77,94,118,137,159,171,178,199,210,221,228,294
# parameters
NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 R_0The r_0 parameter of the switching function=0.25 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 LABELa label for the action so that its output can be referenced in the input to other actions=hbThe COORDINATION action with label hb calculates the following quantities:
 Quantity   
 Type   
 Description  
hb
scalar
the value of the coordination NOPBC ignore the periodic boundary conditions when calculating distances
... COORDINATION
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details ...
# 19 backbone oxygen atoms
GROUPAFirst list of atoms=16,35,56,75,92,116,135,157,169,176,183,197,208,219,226,250,264,278,292 
# 15 backbone hydrogen atoms
GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=18,37,58,77,94,118,137,159,171,178,199,210,221,228,294
# parameters
NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 R_0The r_0 parameter of the switching function=0.25 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 LABELa label for the action so that its output can be referenced in the input to other actions=hb NOPBC ignore the periodic boundary conditions when calculating distances
 D_0 The d_0 parameter of the switching function=0.0
... COORDINATION

# number of hydrophobic contacts
COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details ...
# Cgamma of hydrophobic residues 
GROUPAFirst list of atoms=24,100,124,188,255,269,283
# parameters
NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 R_0The r_0 parameter of the switching function=0.5 LABELa label for the action so that its output can be referenced in the input to other actions=hcThe COORDINATION action with label hc calculates the following quantities:
 Quantity   
 Type   
 Description  
hc
scalar
the value of the coordination NOPBC ignore the periodic boundary conditions when calculating distances
... COORDINATION
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details ...
# Cgamma of hydrophobic residues 
GROUPAFirst list of atoms=24,100,124,188,255,269,283
# parameters
NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 R_0The r_0 parameter of the switching function=0.5 LABELa label for the action so that its output can be referenced in the input to other actions=hc NOPBC ignore the periodic boundary conditions when calculating distances
 D_0 The d_0 parameter of the switching function=0.0
... COORDINATION

# helicity of the backbone
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 ...
# we use as reference for phi,psi -57,-47 
ATOMS1the 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.  REFERENCE1the reference values for each of the torsional angles=-1.0
ATOMS2the 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.  REFERENCE2the reference values for each of the torsional angles=-0.82
ATOMS3the 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.  REFERENCE3the reference values for each of the torsional angles=-1.0
ATOMS4the 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.  REFERENCE4the reference values for each of the torsional angles=-0.82
ATOMS5the 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.  REFERENCE5the reference values for each of the torsional angles=-1.0
ATOMS6the 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.  REFERENCE6the reference values for each of the torsional angles=-0.82
ATOMS7the 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.  REFERENCE7the reference values for each of the torsional angles=-1.0
ATOMS8the 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.  REFERENCE8the reference values for each of the torsional angles=-0.82
ATOMS9the 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.  REFERENCE9the reference values for each of the torsional angles=-1.0
ATOMS10the 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.  REFERENCE10the reference values for each of the torsional angles=-0.82
ATOMS11the 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.  REFERENCE11the reference values for each of the torsional angles=-1.0
ATOMS12the 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.  REFERENCE12the reference values for each of the torsional angles=-0.82
ATOMS13the 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.  REFERENCE13the reference values for each of the torsional angles=-1.0
ATOMS14the 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.  REFERENCE14the reference values for each of the torsional angles=-0.82
ATOMS15the 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.  REFERENCE15the reference values for each of the torsional angles=-1.0
ATOMS16the 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.  REFERENCE16the reference values for each of the torsional angles=-0.82
ATOMS17the 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.  REFERENCE17the reference values for each of the torsional angles=-1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information.  REFERENCE18the reference values for each of the torsional angles=-0.82
ATOMS19the atoms involved for each of the torsions you wish to calculate=@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information.  REFERENCE19the reference values for each of the torsional angles=-1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information.  REFERENCE20the reference values for each of the torsional angles=-0.82
ATOMS21the atoms involved for each of the torsions you wish to calculate=@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information.  REFERENCE21the reference values for each of the torsional angles=-1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information.  REFERENCE22the reference values for each of the torsional angles=-0.82
ATOMS23the atoms involved for each of the torsions you wish to calculate=@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information.  REFERENCE23the reference values for each of the torsional angles=-1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information.  REFERENCE24the reference values for each of the torsional angles=-0.82
ATOMS25the atoms involved for each of the torsions you wish to calculate=@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information.  REFERENCE25the reference values for each of the torsional angles=-1.0
ATOMS26the atoms involved for each of the torsions you wish to calculate=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information.  REFERENCE26the reference values for each of the torsional angles=-0.82
ATOMS27the atoms involved for each of the torsions you wish to calculate=@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information.  REFERENCE27the reference values for each of the torsional angles=-1.0
ATOMS28the atoms involved for each of the torsions you wish to calculate=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information.  REFERENCE28the reference values for each of the torsional angles=-0.82
ATOMS29the atoms involved for each of the torsions you wish to calculate=@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information.  REFERENCE29the reference values for each of the torsional angles=-1.0
ATOMS30the atoms involved for each of the torsions you wish to calculate=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information.  REFERENCE30the reference values for each of the torsional angles=-0.82
ATOMS31the atoms involved for each of the torsions you wish to calculate=@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information.  REFERENCE31the reference values for each of the torsional angles=-1.0
ATOMS32the atoms involved for each of the torsions you wish to calculate=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information.  REFERENCE32the reference values for each of the torsional angles=-0.82
ATOMS33the atoms involved for each of the torsions you wish to calculate=@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information.  REFERENCE33the reference values for each of the torsional angles=-1.0
ATOMS34the atoms involved for each of the torsions you wish to calculate=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information.  REFERENCE34the reference values for each of the torsional angles=-0.82
ATOMS35the atoms involved for each of the torsions you wish to calculate=@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information.  REFERENCE35the reference values for each of the torsional angles=-1.0
ATOMS36the atoms involved for each of the torsions you wish to calculate=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information.  REFERENCE36the reference values for each of the torsional angles=-0.82
LABELa label for the action so that its output can be referenced in the input to other actions=helixThe ALPHABETA action with label helix calculates the following quantities:
 Quantity   
 Type   
 Description  
helix
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# # we use as reference for phi,psi -57,-47 
# ATOMS1=@phi-2 REFERENCE1=-1.0
# ATOMS2=@psi-2 REFERENCE2=-0.82
# ATOMS3=@phi-3 REFERENCE3=-1.0
# ATOMS4=@psi-3 REFERENCE4=-0.82
# ATOMS5=@phi-4 REFERENCE5=-1.0
# ATOMS6=@psi-4 REFERENCE6=-0.82
# ATOMS7=@phi-5 REFERENCE7=-1.0
# ATOMS8=@psi-5 REFERENCE8=-0.82
# ATOMS9=@phi-6 REFERENCE9=-1.0
# ATOMS10=@psi-6 REFERENCE10=-0.82
# ATOMS11=@phi-7 REFERENCE11=-1.0
# ATOMS12=@psi-7 REFERENCE12=-0.82
# ATOMS13=@phi-8 REFERENCE13=-1.0
# ATOMS14=@psi-8 REFERENCE14=-0.82
# ATOMS15=@phi-9 REFERENCE15=-1.0
# ATOMS16=@psi-9 REFERENCE16=-0.82
# ATOMS17=@phi-10 REFERENCE17=-1.0
# ATOMS18=@psi-10 REFERENCE18=-0.82
# ATOMS19=@phi-11 REFERENCE19=-1.0
# ATOMS20=@psi-11 REFERENCE20=-0.82
# ATOMS21=@phi-12 REFERENCE21=-1.0
# ATOMS22=@psi-12 REFERENCE22=-0.82
# ATOMS23=@phi-13 REFERENCE23=-1.0
# ATOMS24=@psi-13 REFERENCE24=-0.82
# ATOMS25=@phi-14 REFERENCE25=-1.0
# ATOMS26=@psi-14 REFERENCE26=-0.82
# ATOMS27=@phi-15 REFERENCE27=-1.0
# ATOMS28=@psi-15 REFERENCE28=-0.82
# ATOMS29=@phi-16 REFERENCE29=-1.0
# ATOMS30=@psi-16 REFERENCE30=-0.82
# ATOMS31=@phi-17 REFERENCE31=-1.0
# ATOMS32=@psi-17 REFERENCE32=-0.82
# ATOMS33=@phi-18 REFERENCE33=-1.0
# ATOMS34=@psi-18 REFERENCE34=-0.82
# ATOMS35=@phi-19 REFERENCE35=-1.0
# ATOMS36=@psi-19 REFERENCE36=-0.82
# LABEL=helix
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
helix_torsionsThe TORSION action with label helix_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
helix_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the 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.  ATOMS2the 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.  ATOMS3the 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.  ATOMS4the 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.  ATOMS5the four atoms involved in the torsional angle=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.      # Action input conctinues with 31 further ATOMSn keywords, 
helix_refThe CONSTANT action with label helix_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
helix_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=-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82,-1.0,-0.82
helix_coeffThe CONSTANT action with label helix_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
helix_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=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
helix_combThe COMBINE action with label helix_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
helix_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=helix_torsions,helix_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
helix_cosThe CUSTOM action with label helix_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
helix_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=helix_comb,helix_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
helixThe SUM action with label helix calculates the following quantities:
 Quantity   
 Type   
 Description  
helix
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=helix_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# beticity of the backbone
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 ...
# we use as reference for phi,psi -80, +150
ATOMS1the 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.  REFERENCE1the reference values for each of the torsional angles=-1.396
ATOMS2the 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.  REFERENCE2the reference values for each of the torsional angles=2.618
ATOMS3the 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.  REFERENCE3the reference values for each of the torsional angles=-1.396
ATOMS4the 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.  REFERENCE4the reference values for each of the torsional angles=2.618
ATOMS5the 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.  REFERENCE5the reference values for each of the torsional angles=-1.396
ATOMS6the 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.  REFERENCE6the reference values for each of the torsional angles=2.618
ATOMS7the 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.  REFERENCE7the reference values for each of the torsional angles=-1.396
ATOMS8the 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.  REFERENCE8the reference values for each of the torsional angles=2.618
ATOMS9the 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.  REFERENCE9the reference values for each of the torsional angles=-1.396
ATOMS10the 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.  REFERENCE10the reference values for each of the torsional angles=2.618
ATOMS11the 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.  REFERENCE11the reference values for each of the torsional angles=-1.396
ATOMS12the 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.  REFERENCE12the reference values for each of the torsional angles=2.618
ATOMS13the 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.  REFERENCE13the reference values for each of the torsional angles=-1.396
ATOMS14the 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.  REFERENCE14the reference values for each of the torsional angles=2.618
ATOMS15the 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.  REFERENCE15the reference values for each of the torsional angles=-1.396
ATOMS16the 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.  REFERENCE16the reference values for each of the torsional angles=2.618
ATOMS17the 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.  REFERENCE17the reference values for each of the torsional angles=-1.396
ATOMS18the atoms involved for each of the torsions you wish to calculate=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information.  REFERENCE18the reference values for each of the torsional angles=2.618
ATOMS19the atoms involved for each of the torsions you wish to calculate=@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information.  REFERENCE19the reference values for each of the torsional angles=-1.396
ATOMS20the atoms involved for each of the torsions you wish to calculate=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information.  REFERENCE20the reference values for each of the torsional angles=2.618
ATOMS21the atoms involved for each of the torsions you wish to calculate=@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information.  REFERENCE21the reference values for each of the torsional angles=-1.396
ATOMS22the atoms involved for each of the torsions you wish to calculate=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information.  REFERENCE22the reference values for each of the torsional angles=2.618
ATOMS23the atoms involved for each of the torsions you wish to calculate=@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information.  REFERENCE23the reference values for each of the torsional angles=-1.396
ATOMS24the atoms involved for each of the torsions you wish to calculate=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information.  REFERENCE24the reference values for each of the torsional angles=2.618
ATOMS25the atoms involved for each of the torsions you wish to calculate=@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information.  REFERENCE25the reference values for each of the torsional angles=-1.396
ATOMS26the atoms involved for each of the torsions you wish to calculate=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information.  REFERENCE26the reference values for each of the torsional angles=2.618
ATOMS27the atoms involved for each of the torsions you wish to calculate=@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information.  REFERENCE27the reference values for each of the torsional angles=-1.396
ATOMS28the atoms involved for each of the torsions you wish to calculate=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information.  REFERENCE28the reference values for each of the torsional angles=2.618
ATOMS29the atoms involved for each of the torsions you wish to calculate=@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information.  REFERENCE29the reference values for each of the torsional angles=-1.396
ATOMS30the atoms involved for each of the torsions you wish to calculate=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information.  REFERENCE30the reference values for each of the torsional angles=2.618
ATOMS31the atoms involved for each of the torsions you wish to calculate=@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information.  REFERENCE31the reference values for each of the torsional angles=-1.396
ATOMS32the atoms involved for each of the torsions you wish to calculate=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information.  REFERENCE32the reference values for each of the torsional angles=2.618
ATOMS33the atoms involved for each of the torsions you wish to calculate=@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information.  REFERENCE33the reference values for each of the torsional angles=-1.396
ATOMS34the atoms involved for each of the torsions you wish to calculate=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information.  REFERENCE34the reference values for each of the torsional angles=2.618
ATOMS35the atoms involved for each of the torsions you wish to calculate=@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information.  REFERENCE35the reference values for each of the torsional angles=-1.396
ATOMS36the atoms involved for each of the torsions you wish to calculate=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information.  REFERENCE36the reference values for each of the torsional angles=2.618
LABELa label for the action so that its output can be referenced in the input to other actions=betaThe ALPHABETA action with label beta calculates the following quantities:
 Quantity   
 Type   
 Description  
beta
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# # we use as reference for phi,psi -80, +150
# ATOMS1=@phi-2 REFERENCE1=-1.396
# ATOMS2=@psi-2 REFERENCE2=2.618
# ATOMS3=@phi-3 REFERENCE3=-1.396
# ATOMS4=@psi-3 REFERENCE4=2.618
# ATOMS5=@phi-4 REFERENCE5=-1.396
# ATOMS6=@psi-4 REFERENCE6=2.618
# ATOMS7=@phi-5 REFERENCE7=-1.396
# ATOMS8=@psi-5 REFERENCE8=2.618
# ATOMS9=@phi-6 REFERENCE9=-1.396
# ATOMS10=@psi-6 REFERENCE10=2.618
# ATOMS11=@phi-7 REFERENCE11=-1.396
# ATOMS12=@psi-7 REFERENCE12=2.618
# ATOMS13=@phi-8 REFERENCE13=-1.396
# ATOMS14=@psi-8 REFERENCE14=2.618
# ATOMS15=@phi-9 REFERENCE15=-1.396
# ATOMS16=@psi-9 REFERENCE16=2.618
# ATOMS17=@phi-10 REFERENCE17=-1.396
# ATOMS18=@psi-10 REFERENCE18=2.618
# ATOMS19=@phi-11 REFERENCE19=-1.396
# ATOMS20=@psi-11 REFERENCE20=2.618
# ATOMS21=@phi-12 REFERENCE21=-1.396
# ATOMS22=@psi-12 REFERENCE22=2.618
# ATOMS23=@phi-13 REFERENCE23=-1.396
# ATOMS24=@psi-13 REFERENCE24=2.618
# ATOMS25=@phi-14 REFERENCE25=-1.396
# ATOMS26=@psi-14 REFERENCE26=2.618
# ATOMS27=@phi-15 REFERENCE27=-1.396
# ATOMS28=@psi-15 REFERENCE28=2.618
# ATOMS29=@phi-16 REFERENCE29=-1.396
# ATOMS30=@psi-16 REFERENCE30=2.618
# ATOMS31=@phi-17 REFERENCE31=-1.396
# ATOMS32=@psi-17 REFERENCE32=2.618
# ATOMS33=@phi-18 REFERENCE33=-1.396
# ATOMS34=@psi-18 REFERENCE34=2.618
# ATOMS35=@phi-19 REFERENCE35=-1.396
# ATOMS36=@psi-19 REFERENCE36=2.618
# LABEL=beta
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
beta_torsionsThe TORSION action with label beta_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
beta_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the 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.  ATOMS2the 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.  ATOMS3the 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.  ATOMS4the 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.  ATOMS5the four atoms involved in the torsional angle=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.      # Action input conctinues with 31 further ATOMSn keywords, 
beta_refThe CONSTANT action with label beta_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
beta_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=-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618,-1.396,2.618
beta_coeffThe CONSTANT action with label beta_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
beta_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=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
beta_combThe COMBINE action with label beta_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
beta_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=beta_torsions,beta_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
beta_cosThe CUSTOM action with label beta_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
beta_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=beta_comb,beta_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
betaThe SUM action with label beta calculates the following quantities:
 Quantity   
 Type   
 Description  
beta
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=beta_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# dihedral correlation
DIHCORMeasures the degree of similarity between dihedral angles. This action is a shortcut. More details ...
ATOMS1the set of 8 atoms that are being used each of the dihedral correlation values=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. ,@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
ATOMS2the set of 8 atoms that are being used each of the dihedral correlation values=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. ,@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
ATOMS3the set of 8 atoms that are being used each of the dihedral correlation values=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. ,@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
ATOMS4the set of 8 atoms that are being used each of the dihedral correlation values=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. ,@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
ATOMS5the set of 8 atoms that are being used each of the dihedral correlation values=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. ,@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
ATOMS6the set of 8 atoms that are being used each of the dihedral correlation values=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. ,@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
ATOMS7the set of 8 atoms that are being used each of the dihedral correlation values=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. ,@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
ATOMS8the set of 8 atoms that are being used each of the dihedral correlation values=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. ,@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
ATOMS9the set of 8 atoms that are being used each of the dihedral correlation values=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. ,@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
ATOMS10the set of 8 atoms that are being used each of the dihedral correlation values=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. ,@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
ATOMS11the set of 8 atoms that are being used each of the dihedral correlation values=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. ,@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
ATOMS12the set of 8 atoms that are being used each of the dihedral correlation values=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. ,@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
ATOMS13the set of 8 atoms that are being used each of the dihedral correlation values=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. ,@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
ATOMS14the set of 8 atoms that are being used each of the dihedral correlation values=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. ,@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. 
ATOMS15the set of 8 atoms that are being used each of the dihedral correlation values=@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. ,@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
ATOMS16the set of 8 atoms that are being used each of the dihedral correlation values=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. ,@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. 
ATOMS17the set of 8 atoms that are being used each of the dihedral correlation values=@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. ,@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
ATOMS18the set of 8 atoms that are being used each of the dihedral correlation values=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. ,@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. 
ATOMS19the set of 8 atoms that are being used each of the dihedral correlation values=@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. ,@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
ATOMS20the set of 8 atoms that are being used each of the dihedral correlation values=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. ,@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. 
ATOMS21the set of 8 atoms that are being used each of the dihedral correlation values=@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. ,@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
ATOMS22the set of 8 atoms that are being used each of the dihedral correlation values=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. ,@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. 
ATOMS23the set of 8 atoms that are being used each of the dihedral correlation values=@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. ,@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
ATOMS24the set of 8 atoms that are being used each of the dihedral correlation values=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. ,@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. 
ATOMS25the set of 8 atoms that are being used each of the dihedral correlation values=@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. ,@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
ATOMS26the set of 8 atoms that are being used each of the dihedral correlation values=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. ,@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. 
ATOMS27the set of 8 atoms that are being used each of the dihedral correlation values=@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. ,@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
ATOMS28the set of 8 atoms that are being used each of the dihedral correlation values=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. ,@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. 
ATOMS29the set of 8 atoms that are being used each of the dihedral correlation values=@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. ,@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
ATOMS30the set of 8 atoms that are being used each of the dihedral correlation values=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. ,@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. 
ATOMS31the set of 8 atoms that are being used each of the dihedral correlation values=@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. ,@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
ATOMS32the set of 8 atoms that are being used each of the dihedral correlation values=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. ,@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. 
ATOMS33the set of 8 atoms that are being used each of the dihedral correlation values=@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. ,@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
ATOMS34the set of 8 atoms that are being used each of the dihedral correlation values=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. ,@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. 
ATOMS35the set of 8 atoms that are being used each of the dihedral correlation values=@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. ,@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
LABELa label for the action so that its output can be referenced in the input to other actions=dihThe DIHCOR action with label dih calculates the following quantities:
 Quantity   
 Type   
 Description  
dih
scalar
the sum of all the dihedral correlations
... DIHCOR
# PLUMED interprets the command:
# DIHCOR ...
# ATOMS1=@phi-2,@psi-2
# ATOMS2=@psi-2,@phi-3
# ATOMS3=@phi-3,@psi-3
# ATOMS4=@psi-3,@phi-4
# ATOMS5=@phi-4,@psi-4
# ATOMS6=@psi-4,@phi-5
# ATOMS7=@phi-5,@psi-5
# ATOMS8=@psi-5,@phi-6
# ATOMS9=@phi-6,@psi-6
# ATOMS10=@psi-6,@phi-7
# ATOMS11=@phi-7,@psi-7
# ATOMS12=@psi-7,@phi-8
# ATOMS13=@phi-8,@psi-8
# ATOMS14=@psi-8,@phi-9
# ATOMS15=@phi-9,@psi-9
# ATOMS16=@psi-9,@phi-10
# ATOMS17=@phi-10,@psi-10
# ATOMS18=@psi-10,@phi-11
# ATOMS19=@phi-11,@psi-11
# ATOMS20=@psi-11,@phi-12
# ATOMS21=@phi-12,@psi-12
# ATOMS22=@psi-12,@phi-13
# ATOMS23=@phi-13,@psi-13
# ATOMS24=@psi-13,@phi-14
# ATOMS25=@phi-14,@psi-14
# ATOMS26=@psi-14,@phi-15
# ATOMS27=@phi-15,@psi-15
# ATOMS28=@psi-15,@phi-16
# ATOMS29=@phi-16,@psi-16
# ATOMS30=@psi-16,@phi-17
# ATOMS31=@phi-17,@psi-17
# ATOMS32=@psi-17,@phi-18
# ATOMS33=@phi-18,@psi-18
# ATOMS34=@psi-18,@phi-19
# ATOMS35=@phi-19,@psi-19
# LABEL=dih
# ... DIHCOR
# as follows (Click the red comment above to revert to the short version of the input):
dih_dataThe DIHEDRAL_CORRELATION action with label dih_data calculates the following quantities:
 Quantity   
 Type   
 Description  
dih_data
vector
the DIHEDRAL_CORRELATION for each set of specified atoms: DIHEDRAL_CORRELATIONMeasure the correlation between a pair of dihedral angles More details ATOMS1the set of 8 atoms that are being used to calculate this quantity=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. ,@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.  ATOMS2the set of 8 atoms that are being used to calculate this quantity=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. ,@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.  ATOMS3the set of 8 atoms that are being used to calculate this quantity=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. ,@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.  ATOMS4the set of 8 atoms that are being used to calculate this quantity=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. ,@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.  ATOMS5the set of 8 atoms that are being used to calculate this quantity=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. ,@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.      # Action input conctinues with 30 further ATOMSn keywords, 
dihThe SUM action with label dih calculates the following quantities:
 Quantity   
 Type   
 Description  
dih
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=dih_data PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# printout
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=rg,hb,hc,helix,beta,dih STRIDE the frequency with which the quantities of interest should be output=500