PLUMED-NEST

Project ID: plumID:19.038
Source: achour2019_mb2m/hb2m/plumed.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#SETTINGS NREPLICAS=2
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
RESTART
Activate restart. More details

#general setup
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=template.pdb
protein: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-1641
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=protein
#collective variables
ab: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=all 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
R_0
The r_0 parameter of the switching function
=0.11 
STRANDS_CUTOFF
If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like
=0.9 
NOPBC
 ignore the periodic boundary conditions

The ANTIBETARMSD action with label ab calculates the following quantities:
 Quantity   
 Description  
ab.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
ab.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
ALPHABETA
Calculate the alpha beta CV More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=abback
REFERENCE
the reference values for each of the torsional angles
=0
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
ATOMS2
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. 
ATOMS3
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. 
ATOMS4
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. 
ATOMS5
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. 
ATOMS6
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. 
ATOMS7
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. 
ATOMS8
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. 
ATOMS9
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. 
ATOMS10
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. 
ATOMS11
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. 
ATOMS12
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. 
ATOMS13
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. 
ATOMS14
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. 
ATOMS15
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. 
ATOMS16
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. 
ATOMS17
the atoms involved for each of the torsions you wish to calculate
=
@psi-20
the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@psi-21
the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
ATOMS19
the atoms involved for each of the torsions you wish to calculate
=
@psi-22
the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
ATOMS20
the atoms involved for each of the torsions you wish to calculate
=
@psi-23
the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
ATOMS21
the atoms involved for each of the torsions you wish to calculate
=
@psi-24
the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
ATOMS22
the atoms involved for each of the torsions you wish to calculate
=
@psi-25
the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
ATOMS23
the atoms involved for each of the torsions you wish to calculate
=
@psi-26
the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
ATOMS24
the atoms involved for each of the torsions you wish to calculate
=
@psi-27
the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
ATOMS25
the atoms involved for each of the torsions you wish to calculate
=
@psi-28
the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
ATOMS26
the atoms involved for each of the torsions you wish to calculate
=
@psi-29
the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
ATOMS27
the atoms involved for each of the torsions you wish to calculate
=
@psi-30
the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
ATOMS28
the atoms involved for each of the torsions you wish to calculate
=
@psi-31
the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
ATOMS29
the atoms involved for each of the torsions you wish to calculate
=
@psi-32
the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
ATOMS30
the atoms involved for each of the torsions you wish to calculate
=
@psi-33
the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
ATOMS31
the atoms involved for each of the torsions you wish to calculate
=
@psi-34
the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
ATOMS32
the atoms involved for each of the torsions you wish to calculate
=
@psi-35
the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
ATOMS33
the atoms involved for each of the torsions you wish to calculate
=
@psi-36
the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
ATOMS34
the atoms involved for each of the torsions you wish to calculate
=
@psi-37
the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
ATOMS35
the atoms involved for each of the torsions you wish to calculate
=
@psi-38
the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
ATOMS36
the atoms involved for each of the torsions you wish to calculate
=
@psi-39
the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
ATOMS37
the atoms involved for each of the torsions you wish to calculate
=
@psi-40
the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
ATOMS38
the atoms involved for each of the torsions you wish to calculate
=
@psi-41
the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
ATOMS39
the atoms involved for each of the torsions you wish to calculate
=
@psi-42
the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information. 
ATOMS40
the atoms involved for each of the torsions you wish to calculate
=
@psi-43
the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information. 
ATOMS41
the atoms involved for each of the torsions you wish to calculate
=
@psi-44
the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information. 
ATOMS42
the atoms involved for each of the torsions you wish to calculate
=
@psi-45
the four atoms that are required to calculate the psi dihedral for residue 45. Click here for more information. 
ATOMS43
the atoms involved for each of the torsions you wish to calculate
=
@psi-46
the four atoms that are required to calculate the psi dihedral for residue 46. Click here for more information. 
ATOMS44
the atoms involved for each of the torsions you wish to calculate
=
@psi-47
the four atoms that are required to calculate the psi dihedral for residue 47. Click here for more information. 
ATOMS45
the atoms involved for each of the torsions you wish to calculate
=
@psi-48
the four atoms that are required to calculate the psi dihedral for residue 48. Click here for more information. 
ATOMS46
the atoms involved for each of the torsions you wish to calculate
=
@psi-49
the four atoms that are required to calculate the psi dihedral for residue 49. Click here for more information. 
ATOMS47
the atoms involved for each of the torsions you wish to calculate
=
@psi-50
the four atoms that are required to calculate the psi dihedral for residue 50. Click here for more information. 
ATOMS48
the atoms involved for each of the torsions you wish to calculate
=
@psi-51
the four atoms that are required to calculate the psi dihedral for residue 51. Click here for more information. 
ATOMS49
the atoms involved for each of the torsions you wish to calculate
=
@psi-52
the four atoms that are required to calculate the psi dihedral for residue 52. Click here for more information. 
ATOMS50
the atoms involved for each of the torsions you wish to calculate
=
@psi-53
the four atoms that are required to calculate the psi dihedral for residue 53. Click here for more information. 
ATOMS51
the atoms involved for each of the torsions you wish to calculate
=
@psi-54
the four atoms that are required to calculate the psi dihedral for residue 54. Click here for more information. 
ATOMS52
the atoms involved for each of the torsions you wish to calculate
=
@psi-55
the four atoms that are required to calculate the psi dihedral for residue 55. Click here for more information. 
ATOMS53
the atoms involved for each of the torsions you wish to calculate
=
@psi-56
the four atoms that are required to calculate the psi dihedral for residue 56. Click here for more information. 
ATOMS54
the atoms involved for each of the torsions you wish to calculate
=
@psi-57
the four atoms that are required to calculate the psi dihedral for residue 57. Click here for more information. 
ATOMS55
the atoms involved for each of the torsions you wish to calculate
=
@psi-58
the four atoms that are required to calculate the psi dihedral for residue 58. Click here for more information. 
ATOMS56
the atoms involved for each of the torsions you wish to calculate
=
@psi-59
the four atoms that are required to calculate the psi dihedral for residue 59. Click here for more information. 
ATOMS57
the atoms involved for each of the torsions you wish to calculate
=
@psi-60
the four atoms that are required to calculate the psi dihedral for residue 60. Click here for more information. 
ATOMS58
the atoms involved for each of the torsions you wish to calculate
=
@psi-61
the four atoms that are required to calculate the psi dihedral for residue 61. Click here for more information. 
ATOMS59
the atoms involved for each of the torsions you wish to calculate
=
@psi-62
the four atoms that are required to calculate the psi dihedral for residue 62. Click here for more information. 
ATOMS60
the atoms involved for each of the torsions you wish to calculate
=
@psi-63
the four atoms that are required to calculate the psi dihedral for residue 63. Click here for more information. 
ATOMS61
the atoms involved for each of the torsions you wish to calculate
=
@psi-64
the four atoms that are required to calculate the psi dihedral for residue 64. Click here for more information. 
ATOMS62
the atoms involved for each of the torsions you wish to calculate
=
@psi-65
the four atoms that are required to calculate the psi dihedral for residue 65. Click here for more information. 
ATOMS63
the atoms involved for each of the torsions you wish to calculate
=
@psi-66
the four atoms that are required to calculate the psi dihedral for residue 66. Click here for more information. 
ATOMS64
the atoms involved for each of the torsions you wish to calculate
=
@psi-67
the four atoms that are required to calculate the psi dihedral for residue 67. Click here for more information. 
ATOMS65
the atoms involved for each of the torsions you wish to calculate
=
@psi-68
the four atoms that are required to calculate the psi dihedral for residue 68. Click here for more information. 
ATOMS66
the atoms involved for each of the torsions you wish to calculate
=
@psi-69
the four atoms that are required to calculate the psi dihedral for residue 69. Click here for more information. 
ATOMS67
the atoms involved for each of the torsions you wish to calculate
=
@psi-70
the four atoms that are required to calculate the psi dihedral for residue 70. Click here for more information. 
ATOMS68
the atoms involved for each of the torsions you wish to calculate
=
@psi-71
the four atoms that are required to calculate the psi dihedral for residue 71. Click here for more information. 
ATOMS69
the atoms involved for each of the torsions you wish to calculate
=
@psi-72
the four atoms that are required to calculate the psi dihedral for residue 72. Click here for more information. 
ATOMS70
the atoms involved for each of the torsions you wish to calculate
=
@psi-73
the four atoms that are required to calculate the psi dihedral for residue 73. Click here for more information. 
ATOMS71
the atoms involved for each of the torsions you wish to calculate
=
@psi-74
the four atoms that are required to calculate the psi dihedral for residue 74. Click here for more information. 
ATOMS72
the atoms involved for each of the torsions you wish to calculate
=
@psi-75
the four atoms that are required to calculate the psi dihedral for residue 75. Click here for more information. 
ATOMS73
the atoms involved for each of the torsions you wish to calculate
=
@psi-76
the four atoms that are required to calculate the psi dihedral for residue 76. Click here for more information. 
ATOMS74
the atoms involved for each of the torsions you wish to calculate
=
@psi-77
the four atoms that are required to calculate the psi dihedral for residue 77. Click here for more information. 
ATOMS75
the atoms involved for each of the torsions you wish to calculate
=
@psi-78
the four atoms that are required to calculate the psi dihedral for residue 78. Click here for more information. 
ATOMS76
the atoms involved for each of the torsions you wish to calculate
=
@psi-79
the four atoms that are required to calculate the psi dihedral for residue 79. Click here for more information. 
ATOMS77
the atoms involved for each of the torsions you wish to calculate
=
@psi-80
the four atoms that are required to calculate the psi dihedral for residue 80. Click here for more information. 
ATOMS78
the atoms involved for each of the torsions you wish to calculate
=
@psi-81
the four atoms that are required to calculate the psi dihedral for residue 81. Click here for more information. 
ATOMS79
the atoms involved for each of the torsions you wish to calculate
=
@psi-82
the four atoms that are required to calculate the psi dihedral for residue 82. Click here for more information. 
ATOMS80
the atoms involved for each of the torsions you wish to calculate
=
@psi-83
the four atoms that are required to calculate the psi dihedral for residue 83. Click here for more information. 
ATOMS81
the atoms involved for each of the torsions you wish to calculate
=
@psi-84
the four atoms that are required to calculate the psi dihedral for residue 84. Click here for more information. 
ATOMS82
the atoms involved for each of the torsions you wish to calculate
=
@psi-85
the four atoms that are required to calculate the psi dihedral for residue 85. Click here for more information. 
ATOMS83
the atoms involved for each of the torsions you wish to calculate
=
@psi-86
the four atoms that are required to calculate the psi dihedral for residue 86. Click here for more information. 
ATOMS84
the atoms involved for each of the torsions you wish to calculate
=
@psi-87
the four atoms that are required to calculate the psi dihedral for residue 87. Click here for more information. 
ATOMS85
the atoms involved for each of the torsions you wish to calculate
=
@psi-88
the four atoms that are required to calculate the psi dihedral for residue 88. Click here for more information. 
ATOMS86
the atoms involved for each of the torsions you wish to calculate
=
@psi-89
the four atoms that are required to calculate the psi dihedral for residue 89. Click here for more information. 
ATOMS87
the atoms involved for each of the torsions you wish to calculate
=
@psi-90
the four atoms that are required to calculate the psi dihedral for residue 90. Click here for more information. 
ATOMS88
the atoms involved for each of the torsions you wish to calculate
=
@psi-91
the four atoms that are required to calculate the psi dihedral for residue 91. Click here for more information. 
ATOMS89
the atoms involved for each of the torsions you wish to calculate
=
@psi-92
the four atoms that are required to calculate the psi dihedral for residue 92. Click here for more information. 
ATOMS90
the atoms involved for each of the torsions you wish to calculate
=
@psi-93
the four atoms that are required to calculate the psi dihedral for residue 93. Click here for more information. 
ATOMS91
the atoms involved for each of the torsions you wish to calculate
=
@psi-94
the four atoms that are required to calculate the psi dihedral for residue 94. Click here for more information. 
ATOMS92
the atoms involved for each of the torsions you wish to calculate
=
@psi-95
the four atoms that are required to calculate the psi dihedral for residue 95. Click here for more information. 
ATOMS93
the atoms involved for each of the torsions you wish to calculate
=
@psi-96
the four atoms that are required to calculate the psi dihedral for residue 96. Click here for more information. 
... ALPHABETA

ALPHABETA
Calculate the alpha beta CV More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=absccore
REFERENCE
the reference values for each of the torsional angles
=0
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@chi1-7
the four atoms that are required to calculate the chi1 dihedral for residue 7. Click here for more information. 
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=
@chi1-8
the four atoms that are required to calculate the chi1 dihedral for residue 8. Click here for more information. 
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=
@chi1-10
the four atoms that are required to calculate the chi1 dihedral for residue 10. Click here for more information. 
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=
@chi1-11
the four atoms that are required to calculate the chi1 dihedral for residue 11. Click here for more information. 
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=
@chi1-17
the four atoms that are required to calculate the chi1 dihedral for residue 17. Click here for more information. 
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=
@chi1-20
the four atoms that are required to calculate the chi1 dihedral for residue 20. Click here for more information. 
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=
@chi1-21
the four atoms that are required to calculate the chi1 dihedral for residue 21. Click here for more information. 
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=
@chi1-22
the four atoms that are required to calculate the chi1 dihedral for residue 22. Click here for more information. 
ATOMS9
the atoms involved for each of the torsions you wish to calculate
=
@chi1-23
the four atoms that are required to calculate the chi1 dihedral for residue 23. Click here for more information. 
ATOMS10
the atoms involved for each of the torsions you wish to calculate
=
@chi1-24
the four atoms that are required to calculate the chi1 dihedral for residue 24. Click here for more information. 
ATOMS11
the atoms involved for each of the torsions you wish to calculate
=
@chi1-25
the four atoms that are required to calculate the chi1 dihedral for residue 25. Click here for more information. 
ATOMS12
the atoms involved for each of the torsions you wish to calculate
=
@chi1-26
the four atoms that are required to calculate the chi1 dihedral for residue 26. Click here for more information. 
ATOMS13
the atoms involved for each of the torsions you wish to calculate
=
@chi1-28
the four atoms that are required to calculate the chi1 dihedral for residue 28. Click here for more information. 
ATOMS14
the atoms involved for each of the torsions you wish to calculate
=
@chi1-30
the four atoms that are required to calculate the chi1 dihedral for residue 30. Click here for more information. 
ATOMS15
the atoms involved for each of the torsions you wish to calculate
=
@chi1-33
the four atoms that are required to calculate the chi1 dihedral for residue 33. Click here for more information. 
ATOMS16
the atoms involved for each of the torsions you wish to calculate
=
@chi1-35
the four atoms that are required to calculate the chi1 dihedral for residue 35. Click here for more information. 
ATOMS17
the atoms involved for each of the torsions you wish to calculate
=
@chi1-39
the four atoms that are required to calculate the chi1 dihedral for residue 39. Click here for more information. 
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@chi1-40
the four atoms that are required to calculate the chi1 dihedral for residue 40. Click here for more information. 
ATOMS19
the atoms involved for each of the torsions you wish to calculate
=
@chi1-42
the four atoms that are required to calculate the chi1 dihedral for residue 42. Click here for more information. 
ATOMS20
the atoms involved for each of the torsions you wish to calculate
=
@chi1-46
the four atoms that are required to calculate the chi1 dihedral for residue 46. Click here for more information. 
ATOMS21
the atoms involved for each of the torsions you wish to calculate
=
@chi1-52
the four atoms that are required to calculate the chi1 dihedral for residue 52. Click here for more information. 
ATOMS22
the atoms involved for each of the torsions you wish to calculate
=
@chi1-54
the four atoms that are required to calculate the chi1 dihedral for residue 54. Click here for more information. 
ATOMS23
the atoms involved for each of the torsions you wish to calculate
=
@chi1-55
the four atoms that are required to calculate the chi1 dihedral for residue 55. Click here for more information. 
ATOMS24
the atoms involved for each of the torsions you wish to calculate
=
@chi1-56
the four atoms that are required to calculate the chi1 dihedral for residue 56. Click here for more information. 
ATOMS25
the atoms involved for each of the torsions you wish to calculate
=
@chi1-57
the four atoms that are required to calculate the chi1 dihedral for residue 57. Click here for more information. 
ATOMS26
the atoms involved for each of the torsions you wish to calculate
=
@chi1-60
the four atoms that are required to calculate the chi1 dihedral for residue 60. Click here for more information. 
ATOMS27
the atoms involved for each of the torsions you wish to calculate
=
@chi1-61
the four atoms that are required to calculate the chi1 dihedral for residue 61. Click here for more information. 
ATOMS28
the atoms involved for each of the torsions you wish to calculate
=
@chi1-62
the four atoms that are required to calculate the chi1 dihedral for residue 62. Click here for more information. 
ATOMS29
the atoms involved for each of the torsions you wish to calculate
=
@chi1-63
the four atoms that are required to calculate the chi1 dihedral for residue 63. Click here for more information. 
ATOMS30
the atoms involved for each of the torsions you wish to calculate
=
@chi1-64
the four atoms that are required to calculate the chi1 dihedral for residue 64. Click here for more information. 
ATOMS31
the atoms involved for each of the torsions you wish to calculate
=
@chi1-65
the four atoms that are required to calculate the chi1 dihedral for residue 65. Click here for more information. 
ATOMS32
the atoms involved for each of the torsions you wish to calculate
=
@chi1-66
the four atoms that are required to calculate the chi1 dihedral for residue 66. Click here for more information. 
ATOMS33
the atoms involved for each of the torsions you wish to calculate
=
@chi1-67
the four atoms that are required to calculate the chi1 dihedral for residue 67. Click here for more information. 
ATOMS34
the atoms involved for each of the torsions you wish to calculate
=
@chi1-68
the four atoms that are required to calculate the chi1 dihedral for residue 68. Click here for more information. 
ATOMS35
the atoms involved for each of the torsions you wish to calculate
=
@chi1-70
the four atoms that are required to calculate the chi1 dihedral for residue 70. Click here for more information. 
ATOMS36
the atoms involved for each of the torsions you wish to calculate
=
@chi1-71
the four atoms that are required to calculate the chi1 dihedral for residue 71. Click here for more information. 
ATOMS37
the atoms involved for each of the torsions you wish to calculate
=
@chi1-73
the four atoms that are required to calculate the chi1 dihedral for residue 73. Click here for more information. 
ATOMS38
the atoms involved for each of the torsions you wish to calculate
=
@chi1-78
the four atoms that are required to calculate the chi1 dihedral for residue 78. Click here for more information. 
ATOMS39
the atoms involved for each of the torsions you wish to calculate
=
@chi1-80
the four atoms that are required to calculate the chi1 dihedral for residue 80. Click here for more information. 
ATOMS40
the atoms involved for each of the torsions you wish to calculate
=
@chi1-83
the four atoms that are required to calculate the chi1 dihedral for residue 83. Click here for more information. 
ATOMS41
the atoms involved for each of the torsions you wish to calculate
=
@chi1-86
the four atoms that are required to calculate the chi1 dihedral for residue 86. Click here for more information. 
ATOMS42
the atoms involved for each of the torsions you wish to calculate
=
@chi1-87
the four atoms that are required to calculate the chi1 dihedral for residue 87. Click here for more information. 
ATOMS43
the atoms involved for each of the torsions you wish to calculate
=
@chi1-88
the four atoms that are required to calculate the chi1 dihedral for residue 88. Click here for more information. 
ATOMS44
the atoms involved for each of the torsions you wish to calculate
=
@chi1-89
the four atoms that are required to calculate the chi1 dihedral for residue 89. Click here for more information. 
ATOMS45
the atoms involved for each of the torsions you wish to calculate
=
@chi1-92
the four atoms that are required to calculate the chi1 dihedral for residue 92. Click here for more information. 
ATOMS46
the atoms involved for each of the torsions you wish to calculate
=
@chi1-95
the four atoms that are required to calculate the chi1 dihedral for residue 95. Click here for more information. 
... ALPHABETA

ALPHABETA
Calculate the alpha beta CV More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=abscsurf
REFERENCE
the reference values for each of the torsional angles
=0
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@chi1-3
the four atoms that are required to calculate the chi1 dihedral for residue 3. Click here for more information. 
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=
@chi1-6
the four atoms that are required to calculate the chi1 dihedral for residue 6. Click here for more information. 
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=
@chi1-12
the four atoms that are required to calculate the chi1 dihedral for residue 12. Click here for more information. 
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=
@chi1-13
the four atoms that are required to calculate the chi1 dihedral for residue 13. Click here for more information. 
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=
@chi1-16
the four atoms that are required to calculate the chi1 dihedral for residue 16. Click here for more information. 
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=
@chi1-19
the four atoms that are required to calculate the chi1 dihedral for residue 19. Click here for more information. 
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=
@chi1-31
the four atoms that are required to calculate the chi1 dihedral for residue 31. Click here for more information. 
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=
@chi1-34
the four atoms that are required to calculate the chi1 dihedral for residue 34. Click here for more information. 
ATOMS9
the atoms involved for each of the torsions you wish to calculate
=
@chi1-36
the four atoms that are required to calculate the chi1 dihedral for residue 36. Click here for more information. 
ATOMS10
the atoms involved for each of the torsions you wish to calculate
=
@chi1-38
the four atoms that are required to calculate the chi1 dihedral for residue 38. Click here for more information. 
ATOMS11
the atoms involved for each of the torsions you wish to calculate
=
@chi1-41
the four atoms that are required to calculate the chi1 dihedral for residue 41. Click here for more information. 
ATOMS12
the atoms involved for each of the torsions you wish to calculate
=
@chi1-44
the four atoms that are required to calculate the chi1 dihedral for residue 44. Click here for more information. 
ATOMS13
the atoms involved for each of the torsions you wish to calculate
=
@chi1-45
the four atoms that are required to calculate the chi1 dihedral for residue 45. Click here for more information. 
ATOMS14
the atoms involved for each of the torsions you wish to calculate
=
@chi1-47
the four atoms that are required to calculate the chi1 dihedral for residue 47. Click here for more information. 
ATOMS15
the atoms involved for each of the torsions you wish to calculate
=
@chi1-48
the four atoms that are required to calculate the chi1 dihedral for residue 48. Click here for more information. 
ATOMS16
the atoms involved for each of the torsions you wish to calculate
=
@chi1-50
the four atoms that are required to calculate the chi1 dihedral for residue 50. Click here for more information. 
ATOMS17
the atoms involved for each of the torsions you wish to calculate
=
@chi1-51
the four atoms that are required to calculate the chi1 dihedral for residue 51. Click here for more information. 
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@chi1-53
the four atoms that are required to calculate the chi1 dihedral for residue 53. Click here for more information. 
ATOMS19
the atoms involved for each of the torsions you wish to calculate
=
@chi1-58
the four atoms that are required to calculate the chi1 dihedral for residue 58. Click here for more information. 
ATOMS20
the atoms involved for each of the torsions you wish to calculate
=
@chi1-59
the four atoms that are required to calculate the chi1 dihedral for residue 59. Click here for more information. 
ATOMS21
the atoms involved for each of the torsions you wish to calculate
=
@chi1-69
the four atoms that are required to calculate the chi1 dihedral for residue 69. Click here for more information. 
ATOMS22
the atoms involved for each of the torsions you wish to calculate
=
@chi1-74
the four atoms that are required to calculate the chi1 dihedral for residue 74. Click here for more information. 
ATOMS23
the atoms involved for each of the torsions you wish to calculate
=
@chi1-75
the four atoms that are required to calculate the chi1 dihedral for residue 75. Click here for more information. 
ATOMS24
the atoms involved for each of the torsions you wish to calculate
=
@chi1-76
the four atoms that are required to calculate the chi1 dihedral for residue 76. Click here for more information. 
ATOMS25
the atoms involved for each of the torsions you wish to calculate
=
@chi1-77
the four atoms that are required to calculate the chi1 dihedral for residue 77. Click here for more information. 
ATOMS26
the atoms involved for each of the torsions you wish to calculate
=
@chi1-81
the four atoms that are required to calculate the chi1 dihedral for residue 81. Click here for more information. 
ATOMS27
the atoms involved for each of the torsions you wish to calculate
=
@chi1-84
the four atoms that are required to calculate the chi1 dihedral for residue 84. Click here for more information. 
ATOMS28
the atoms involved for each of the torsions you wish to calculate
=
@chi1-91
the four atoms that are required to calculate the chi1 dihedral for residue 91. Click here for more information. 
ATOMS29
the atoms involved for each of the torsions you wish to calculate
=
@chi1-94
the four atoms that are required to calculate the chi1 dihedral for residue 94. Click here for more information. 
ATOMS30
the atoms involved for each of the torsions you wish to calculate
=
@chi1-96
the four atoms that are required to calculate the chi1 dihedral for residue 96. Click here for more information. 
ATOMS31
the atoms involved for each of the torsions you wish to calculate
=
@chi1-97
the four atoms that are required to calculate the chi1 dihedral for residue 97. Click here for more information. 
ATOMS32
the atoms involved for each of the torsions you wish to calculate
=
@chi1-98
the four atoms that are required to calculate the chi1 dihedral for residue 98. Click here for more information. 
... ALPHABETA

PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=mm
ARG
the input for this action is the scalar output from one or more other actions
=ab,abback,absccore,abscsurf
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
SIGMA
the widths of the Gaussian hills
=2000
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.1,0.12,0.12,0.12 
PACE
the frequency for hill addition, one for all biases
=200 
HEIGHT
the height of the Gaussian hills, one for all biases
=1.0 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=20 
GRID_MIN
the lower bounds for the grid
=10,0,0,0 
GRID_MAX
the upper bounds for the grid
=35,60,50,40 
INTERVAL_MIN
one dimensional lower limits, outside the limits the system will not feel the biasing force
=12,10,10,0 
INTERVAL_MAX
one dimensional upper limits, outside the limits the system will not feel the biasing force
=30,42,40,33 
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
GRID_WSTRIDE
frequency for dumping the grid
=10000
#GRID_RFILES=GRID.ab,GRID.abback,GRID.absccore,GRID.abscsurf
... PBMETAD

The PBMETAD action with label mm calculates the following quantities:
 Quantity   
 Description  
mm.bias
the instantaneous value of the bias potential
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=ab,abback,absccore 
AT
the positions of the wall
=12,10,10 
KAPPA
the force constant for the wall
=500,200,200
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=ab,abback,absccore 
AT
the positions of the wall
=30,42,40 
KAPPA
the force constant for the wall
=500,200,200

# experimental data
meta_ca: 
CS2BACKBONE
Calculates the backbone chemical shifts for a protein. More details
 
ATOMS
The atoms to be included in the calculation, e
=protein 
DATADIR
 The folder with the experimental chemical shifts
=data_ca 
TEMPLATE
 A PDB file of the protein system
=template.pdb 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
DOSCORE
 activate metainference
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200 
ARG
the input for this action is the scalar output from one or more other actions
=mm.bias 
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.01 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=OUTLIERS
The CS2BACKBONE action with label meta_ca calculates the following quantities:
 Quantity   
 Description  
meta_ca.score
the Metainference score
meta_ca.sigma
uncertainty parameter
meta_ca.sigmaMean
uncertainty in the mean estimate
meta_ca.neff
effective number of replicas
meta_ca.acceptSigma
MC acceptance for sigma values
meta_ca.weight
weights of the weighted average
meta_ca.biasDer
derivatives with respect to the bias
meta_ca.ha
the calculated Ha hydrogen chemical shifts
meta_ca.hn
the calculated H hydrogen chemical shifts
meta_ca.nh
the calculated N nitrogen chemical shifts
meta_ca.ca
the calculated Ca carbon chemical shifts
meta_ca.cb
the calculated Cb carbon chemical shifts
meta_ca.co
the calculated C' carbon chemical shifts
meta_ca.expha
the experimental Ha hydrogen chemical shifts
meta_ca.exphn
the experimental H hydrogen chemical shifts
meta_ca.expnh
the experimental N nitrogen chemical shifts
meta_ca.expca
the experimental Ca carbon chemical shifts
meta_ca.expcb
the experimental Cb carbon chemical shifts
meta_ca.expco
the experimental C' carbon chemical shiftsmeta_cb: 
CS2BACKBONE
Calculates the backbone chemical shifts for a protein. More details
 
ATOMS
The atoms to be included in the calculation, e
=protein 
DATADIR
 The folder with the experimental chemical shifts
=data_cb 
TEMPLATE
 A PDB file of the protein system
=template.pdb 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
DOSCORE
 activate metainference
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200 
ARG
the input for this action is the scalar output from one or more other actions
=mm.bias 
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.01 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=OUTLIERS
The CS2BACKBONE action with label meta_cb calculates the following quantities:
 Quantity   
 Description  
meta_cb.score
the Metainference score
meta_cb.sigma
uncertainty parameter
meta_cb.sigmaMean
uncertainty in the mean estimate
meta_cb.neff
effective number of replicas
meta_cb.acceptSigma
MC acceptance for sigma values
meta_cb.weight
weights of the weighted average
meta_cb.biasDer
derivatives with respect to the bias
meta_cb.ha
the calculated Ha hydrogen chemical shifts
meta_cb.hn
the calculated H hydrogen chemical shifts
meta_cb.nh
the calculated N nitrogen chemical shifts
meta_cb.ca
the calculated Ca carbon chemical shifts
meta_cb.cb
the calculated Cb carbon chemical shifts
meta_cb.co
the calculated C' carbon chemical shifts
meta_cb.expha
the experimental Ha hydrogen chemical shifts
meta_cb.exphn
the experimental H hydrogen chemical shifts
meta_cb.expnh
the experimental N nitrogen chemical shifts
meta_cb.expca
the experimental Ca carbon chemical shifts
meta_cb.expcb
the experimental Cb carbon chemical shifts
meta_cb.expco
the experimental C' carbon chemical shiftsmeta_co: 
CS2BACKBONE
Calculates the backbone chemical shifts for a protein. More details
 
ATOMS
The atoms to be included in the calculation, e
=protein 
DATADIR
 The folder with the experimental chemical shifts
=data_co 
TEMPLATE
 A PDB file of the protein system
=template.pdb 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
DOSCORE
 activate metainference
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200 
ARG
the input for this action is the scalar output from one or more other actions
=mm.bias 
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.01 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=OUTLIERS
The CS2BACKBONE action with label meta_co calculates the following quantities:
 Quantity   
 Description  
meta_co.score
the Metainference score
meta_co.sigma
uncertainty parameter
meta_co.sigmaMean
uncertainty in the mean estimate
meta_co.neff
effective number of replicas
meta_co.acceptSigma
MC acceptance for sigma values
meta_co.weight
weights of the weighted average
meta_co.biasDer
derivatives with respect to the bias
meta_co.ha
the calculated Ha hydrogen chemical shifts
meta_co.hn
the calculated H hydrogen chemical shifts
meta_co.nh
the calculated N nitrogen chemical shifts
meta_co.ca
the calculated Ca carbon chemical shifts
meta_co.cb
the calculated Cb carbon chemical shifts
meta_co.co
the calculated C' carbon chemical shifts
meta_co.expha
the experimental Ha hydrogen chemical shifts
meta_co.exphn
the experimental H hydrogen chemical shifts
meta_co.expnh
the experimental N nitrogen chemical shifts
meta_co.expca
the experimental Ca carbon chemical shifts
meta_co.expcb
the experimental Cb carbon chemical shifts
meta_co.expco
the experimental C' carbon chemical shiftsmeta_hn: 
CS2BACKBONE
Calculates the backbone chemical shifts for a protein. More details
 
ATOMS
The atoms to be included in the calculation, e
=protein 
DATADIR
 The folder with the experimental chemical shifts
=data_hn 
TEMPLATE
 A PDB file of the protein system
=template.pdb 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
DOSCORE
 activate metainference
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200 
ARG
the input for this action is the scalar output from one or more other actions
=mm.bias 
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.01 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=OUTLIERS
The CS2BACKBONE action with label meta_hn calculates the following quantities:
 Quantity   
 Description  
meta_hn.score
the Metainference score
meta_hn.sigma
uncertainty parameter
meta_hn.sigmaMean
uncertainty in the mean estimate
meta_hn.neff
effective number of replicas
meta_hn.acceptSigma
MC acceptance for sigma values
meta_hn.weight
weights of the weighted average
meta_hn.biasDer
derivatives with respect to the bias
meta_hn.ha
the calculated Ha hydrogen chemical shifts
meta_hn.hn
the calculated H hydrogen chemical shifts
meta_hn.nh
the calculated N nitrogen chemical shifts
meta_hn.ca
the calculated Ca carbon chemical shifts
meta_hn.cb
the calculated Cb carbon chemical shifts
meta_hn.co
the calculated C' carbon chemical shifts
meta_hn.expha
the experimental Ha hydrogen chemical shifts
meta_hn.exphn
the experimental H hydrogen chemical shifts
meta_hn.expnh
the experimental N nitrogen chemical shifts
meta_hn.expca
the experimental Ca carbon chemical shifts
meta_hn.expcb
the experimental Cb carbon chemical shifts
meta_hn.expco
the experimental C' carbon chemical shiftsmeta_nh: 
CS2BACKBONE
Calculates the backbone chemical shifts for a protein. More details
 
ATOMS
The atoms to be included in the calculation, e
=protein 
DATADIR
 The folder with the experimental chemical shifts
=data_nh 
TEMPLATE
 A PDB file of the protein system
=template.pdb 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
DOSCORE
 activate metainference
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200 
ARG
the input for this action is the scalar output from one or more other actions
=mm.bias 
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.01 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=OUTLIERS

The CS2BACKBONE action with label meta_nh calculates the following quantities:
 Quantity   
 Description  
meta_nh.score
the Metainference score
meta_nh.sigma
uncertainty parameter
meta_nh.sigmaMean
uncertainty in the mean estimate
meta_nh.neff
effective number of replicas
meta_nh.acceptSigma
MC acceptance for sigma values
meta_nh.weight
weights of the weighted average
meta_nh.biasDer
derivatives with respect to the bias
meta_nh.ha
the calculated Ha hydrogen chemical shifts
meta_nh.hn
the calculated H hydrogen chemical shifts
meta_nh.nh
the calculated N nitrogen chemical shifts
meta_nh.ca
the calculated Ca carbon chemical shifts
meta_nh.cb
the calculated Cb carbon chemical shifts
meta_nh.co
the calculated C' carbon chemical shifts
meta_nh.expha
the experimental Ha hydrogen chemical shifts
meta_nh.exphn
the experimental H hydrogen chemical shifts
meta_nh.expnh
the experimental N nitrogen chemical shifts
meta_nh.expca
the experimental Ca carbon chemical shifts
meta_nh.expcb
the experimental Cb carbon chemical shifts
meta_nh.expco
the experimental C' carbon chemical shifts
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=meta_ca.score,meta_cb.score,meta_co.score,meta_hn.score,meta_nh.score

The BIASVALUE action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ab,abback,absccore,abscsurf,mm.bias 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=200
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=meta_ca.score,meta_ca.biasDer,meta_ca.weight,meta_ca.acceptSigma,meta_ca.sigmaMean,meta_ca.sigma 
FILE
the name of the file on which to output these quantities
=MI_CS_CA.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=2000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=meta_cb.score,meta_cb.biasDer,meta_cb.weight,meta_cb.acceptSigma,meta_cb.sigmaMean,meta_cb.sigma 
FILE
the name of the file on which to output these quantities
=MI_CS_CB.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=2000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=meta_co.score,meta_co.biasDer,meta_co.weight,meta_co.acceptSigma,meta_co.sigmaMean,meta_co.sigma 
FILE
the name of the file on which to output these quantities
=MI_CS_CO.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=2000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=meta_hn.score,meta_hn.biasDer,meta_hn.weight,meta_hn.acceptSigma,meta_hn.sigmaMean,meta_hn.sigma 
FILE
the name of the file on which to output these quantities
=MI_CS_HN.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=2000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=meta_nh.score,meta_nh.biasDer,meta_nh.weight,meta_nh.acceptSigma,meta_nh.sigmaMean,meta_nh.sigma 
FILE
the name of the file on which to output these quantities
=MI_CS_NH.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=2000

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=10000
ENDPLUMED
Terminate plumed input. More details