PLUMED-NEST

Project ID: plumID:20.020
Source: plumed.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

# include definition of CVs
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=plumed_cv.dat
# The command:
# INCLUDE FILE=plumed_cv.dat
# ensures PLUMED loads the contents of the file called plumed_cv.dat
# The contents of this file are shown below (click the red comment to hide them).
# protein info
The INCLUDE action with label plumed_cv.dat calculates something
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
=trp.pdb

# whole molecule for all the backbone atoms
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
 
RESIDUES
this command specifies that the backbone atoms in a set of residues all must be aligned
=all 
MOLTYPE
the 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: 
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
=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
COORDINATION
Calculate coordination numbers. More details
 ...
# 19 backbone oxygen atoms
GROUPA
First 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
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.25 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=0.8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 
LABEL
a 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

# number of hydrophobic contacts
COORDINATION
Calculate coordination numbers. More details
 ...
# Cgamma of hydrophobic residues 
GROUPA
First 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_0
The r_0 parameter of the switching function
=0.5 
LABEL
a 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

# helicity of the backbone
ALPHABETA
Calculate the alpha beta CV More details
 ...
# we use as reference for phi,psi -57,-47 
ATOMS1
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. 
 
REFERENCE1
the reference values for each of the torsional angles
=-1.0
ATOMS2
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. 
 
REFERENCE2
the reference values for each of the torsional angles
=-0.82
ATOMS3
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. 
 
REFERENCE3
the reference values for each of the torsional angles
=-1.0
ATOMS4
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. 
 
REFERENCE4
the reference values for each of the torsional angles
=-0.82
ATOMS5
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. 
 
REFERENCE5
the reference values for each of the torsional angles
=-1.0
ATOMS6
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. 
 
REFERENCE6
the reference values for each of the torsional angles
=-0.82
ATOMS7
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. 
 
REFERENCE7
the reference values for each of the torsional angles
=-1.0
ATOMS8
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. 
 
REFERENCE8
the reference values for each of the torsional angles
=-0.82
ATOMS9
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. 
 
REFERENCE9
the reference values for each of the torsional angles
=-1.0
ATOMS10
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. 
 
REFERENCE10
the reference values for each of the torsional angles
=-0.82
ATOMS11
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. 
 
REFERENCE11
the reference values for each of the torsional angles
=-1.0
ATOMS12
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. 
 
REFERENCE12
the reference values for each of the torsional angles
=-0.82
ATOMS13
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. 
 
REFERENCE13
the reference values for each of the torsional angles
=-1.0
ATOMS14
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. 
 
REFERENCE14
the reference values for each of the torsional angles
=-0.82
ATOMS15
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. 
 
REFERENCE15
the reference values for each of the torsional angles
=-1.0
ATOMS16
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. 
 
REFERENCE16
the reference values for each of the torsional angles
=-0.82
ATOMS17
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. 
 
REFERENCE17
the reference values for each of the torsional angles
=-1.0
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
 
REFERENCE18
the reference values for each of the torsional angles
=-0.82
ATOMS19
the atoms involved for each of the torsions you wish to calculate
=
@phi-11
the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. 
 
REFERENCE19
the reference values for each of the torsional angles
=-1.0
ATOMS20
the atoms involved for each of the torsions you wish to calculate
=
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
 
REFERENCE20
the reference values for each of the torsional angles
=-0.82
ATOMS21
the atoms involved for each of the torsions you wish to calculate
=
@phi-12
the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. 
 
REFERENCE21
the reference values for each of the torsional angles
=-1.0
ATOMS22
the atoms involved for each of the torsions you wish to calculate
=
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
 
REFERENCE22
the reference values for each of the torsional angles
=-0.82
ATOMS23
the atoms involved for each of the torsions you wish to calculate
=
@phi-13
the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. 
 
REFERENCE23
the reference values for each of the torsional angles
=-1.0
ATOMS24
the atoms involved for each of the torsions you wish to calculate
=
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
 
REFERENCE24
the reference values for each of the torsional angles
=-0.82
ATOMS25
the atoms involved for each of the torsions you wish to calculate
=
@phi-14
the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. 
 
REFERENCE25
the reference values for each of the torsional angles
=-1.0
ATOMS26
the atoms involved for each of the torsions you wish to calculate
=
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
 
REFERENCE26
the reference values for each of the torsional angles
=-0.82
ATOMS27
the atoms involved for each of the torsions you wish to calculate
=
@phi-15
the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. 
 
REFERENCE27
the reference values for each of the torsional angles
=-1.0
ATOMS28
the atoms involved for each of the torsions you wish to calculate
=
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
 
REFERENCE28
the reference values for each of the torsional angles
=-0.82
ATOMS29
the atoms involved for each of the torsions you wish to calculate
=
@phi-16
the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. 
 
REFERENCE29
the reference values for each of the torsional angles
=-1.0
ATOMS30
the atoms involved for each of the torsions you wish to calculate
=
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
 
REFERENCE30
the reference values for each of the torsional angles
=-0.82
ATOMS31
the atoms involved for each of the torsions you wish to calculate
=
@phi-17
the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. 
 
REFERENCE31
the reference values for each of the torsional angles
=-1.0
ATOMS32
the atoms involved for each of the torsions you wish to calculate
=
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
 
REFERENCE32
the reference values for each of the torsional angles
=-0.82
ATOMS33
the atoms involved for each of the torsions you wish to calculate
=
@phi-18
the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. 
 
REFERENCE33
the reference values for each of the torsional angles
=-1.0
ATOMS34
the atoms involved for each of the torsions you wish to calculate
=
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
 
REFERENCE34
the reference values for each of the torsional angles
=-0.82
ATOMS35
the atoms involved for each of the torsions you wish to calculate
=
@phi-19
the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. 
 
REFERENCE35
the reference values for each of the torsional angles
=-1.0
ATOMS36
the atoms involved for each of the torsions you wish to calculate
=
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
 
REFERENCE36
the reference values for each of the torsional angles
=-0.82
LABEL
a label for the action so that its output can be referenced in the input to other actions
=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
... ALPHABETA

# beticity of the backbone
ALPHABETA
Calculate the alpha beta CV More details
 ...
# we use as reference for phi,psi -80, +150
ATOMS1
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. 
 
REFERENCE1
the reference values for each of the torsional angles
=-1.396
ATOMS2
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. 
 
REFERENCE2
the reference values for each of the torsional angles
=2.618
ATOMS3
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. 
 
REFERENCE3
the reference values for each of the torsional angles
=-1.396
ATOMS4
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. 
 
REFERENCE4
the reference values for each of the torsional angles
=2.618
ATOMS5
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. 
 
REFERENCE5
the reference values for each of the torsional angles
=-1.396
ATOMS6
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. 
 
REFERENCE6
the reference values for each of the torsional angles
=2.618
ATOMS7
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. 
 
REFERENCE7
the reference values for each of the torsional angles
=-1.396
ATOMS8
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. 
 
REFERENCE8
the reference values for each of the torsional angles
=2.618
ATOMS9
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. 
 
REFERENCE9
the reference values for each of the torsional angles
=-1.396
ATOMS10
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. 
 
REFERENCE10
the reference values for each of the torsional angles
=2.618
ATOMS11
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. 
 
REFERENCE11
the reference values for each of the torsional angles
=-1.396
ATOMS12
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. 
 
REFERENCE12
the reference values for each of the torsional angles
=2.618
ATOMS13
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. 
 
REFERENCE13
the reference values for each of the torsional angles
=-1.396
ATOMS14
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. 
 
REFERENCE14
the reference values for each of the torsional angles
=2.618
ATOMS15
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. 
 
REFERENCE15
the reference values for each of the torsional angles
=-1.396
ATOMS16
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. 
 
REFERENCE16
the reference values for each of the torsional angles
=2.618
ATOMS17
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. 
 
REFERENCE17
the reference values for each of the torsional angles
=-1.396
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
 
REFERENCE18
the reference values for each of the torsional angles
=2.618
ATOMS19
the atoms involved for each of the torsions you wish to calculate
=
@phi-11
the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. 
 
REFERENCE19
the reference values for each of the torsional angles
=-1.396
ATOMS20
the atoms involved for each of the torsions you wish to calculate
=
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
 
REFERENCE20
the reference values for each of the torsional angles
=2.618
ATOMS21
the atoms involved for each of the torsions you wish to calculate
=
@phi-12
the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. 
 
REFERENCE21
the reference values for each of the torsional angles
=-1.396
ATOMS22
the atoms involved for each of the torsions you wish to calculate
=
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
 
REFERENCE22
the reference values for each of the torsional angles
=2.618
ATOMS23
the atoms involved for each of the torsions you wish to calculate
=
@phi-13
the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. 
 
REFERENCE23
the reference values for each of the torsional angles
=-1.396
ATOMS24
the atoms involved for each of the torsions you wish to calculate
=
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
 
REFERENCE24
the reference values for each of the torsional angles
=2.618
ATOMS25
the atoms involved for each of the torsions you wish to calculate
=
@phi-14
the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. 
 
REFERENCE25
the reference values for each of the torsional angles
=-1.396
ATOMS26
the atoms involved for each of the torsions you wish to calculate
=
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
 
REFERENCE26
the reference values for each of the torsional angles
=2.618
ATOMS27
the atoms involved for each of the torsions you wish to calculate
=
@phi-15
the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. 
 
REFERENCE27
the reference values for each of the torsional angles
=-1.396
ATOMS28
the atoms involved for each of the torsions you wish to calculate
=
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
 
REFERENCE28
the reference values for each of the torsional angles
=2.618
ATOMS29
the atoms involved for each of the torsions you wish to calculate
=
@phi-16
the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. 
 
REFERENCE29
the reference values for each of the torsional angles
=-1.396
ATOMS30
the atoms involved for each of the torsions you wish to calculate
=
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
 
REFERENCE30
the reference values for each of the torsional angles
=2.618
ATOMS31
the atoms involved for each of the torsions you wish to calculate
=
@phi-17
the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. 
 
REFERENCE31
the reference values for each of the torsional angles
=-1.396
ATOMS32
the atoms involved for each of the torsions you wish to calculate
=
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
 
REFERENCE32
the reference values for each of the torsional angles
=2.618
ATOMS33
the atoms involved for each of the torsions you wish to calculate
=
@phi-18
the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. 
 
REFERENCE33
the reference values for each of the torsional angles
=-1.396
ATOMS34
the atoms involved for each of the torsions you wish to calculate
=
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
 
REFERENCE34
the reference values for each of the torsional angles
=2.618
ATOMS35
the atoms involved for each of the torsions you wish to calculate
=
@phi-19
the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. 
 
REFERENCE35
the reference values for each of the torsional angles
=-1.396
ATOMS36
the atoms involved for each of the torsions you wish to calculate
=
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
 
REFERENCE36
the reference values for each of the torsional angles
=2.618
LABEL
a label for the action so that its output can be referenced in the input to other actions
=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
... ALPHABETA

# dihedral correlation
DIHCOR
Measures the degree of similarity between dihedral angles. More details
 ...
ATOMS1
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
,
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
ATOMS2
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
,
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
ATOMS3
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
,
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
ATOMS4
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
,
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
ATOMS5
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
,
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
ATOMS6
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
,
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
ATOMS7
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
,
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
ATOMS8
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
,
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
ATOMS9
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
,
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
ATOMS10
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
,
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
ATOMS11
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
,
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
ATOMS12
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
,
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
ATOMS13
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
,
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
ATOMS14
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
,
@phi-9
the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. 
ATOMS15
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-9
the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. 
,
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
ATOMS16
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
,
@phi-10
the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. 
ATOMS17
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-10
the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. 
,
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
ATOMS18
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
,
@phi-11
the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. 
ATOMS19
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-11
the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. 
,
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
ATOMS20
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
,
@phi-12
the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. 
ATOMS21
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-12
the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. 
,
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
ATOMS22
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
,
@phi-13
the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. 
ATOMS23
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-13
the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. 
,
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
ATOMS24
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
,
@phi-14
the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. 
ATOMS25
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-14
the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. 
,
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
ATOMS26
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
,
@phi-15
the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. 
ATOMS27
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-15
the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. 
,
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
ATOMS28
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
,
@phi-16
the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. 
ATOMS29
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-16
the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. 
,
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
ATOMS30
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
,
@phi-17
the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. 
ATOMS31
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-17
the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. 
,
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
ATOMS32
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
,
@phi-18
the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. 
ATOMS33
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-18
the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. 
,
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
ATOMS34
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
,
@phi-19
the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. 
ATOMS35
the set of 8 atoms that are being used each of the dihedral correlation values
=
@phi-19
the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. 
,
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=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
... DIHCOR

# printout
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=rg,hb,hc,helix,beta,dih 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
# --- End of included input --- 
# Parallel-bias metadynamics
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=rg,hb,hc,helix,beta,dih
PACE
the frequency for hill addition, one for all biases
=500 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=8.0 
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
SIGMA
the widths of the Gaussian hills
=0.01,0.6,0.3,0.4,0.3,0.6
GRID_MIN
the lower bounds for the grid
=0.4,0.0,0.0,0.0,0.0,0.0
GRID_MAX
the upper bounds for the grid
=2.0,100.0,25.0,40.0,40.0,40.0
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS_rg,HILLS_hb,HILLS_hc,HILLS_helix,HILLS_beta,HILLS_dih 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe PBMETAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
... PBMETAD