PLUMED-NEST

Project ID: plumID:19.029
Source: C57D.plumed2/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

# restart previous simulation
# RESTART
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
=reference.pdb 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=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
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=protein

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
#index group for C-alpha needed for Rg
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
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=C-alpha 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c_alphas

GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
TYPE
 The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=c_alphas 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rg_ca #Ca Rg CV1

ALPHABETA
Calculate the alpha beta CV More details
 ...
ATOMS1
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. 
 
REFERENCE
the reference values for each of the torsional angles
=-0.78540  # for psi alphahelix app -45 deg CV2 alpha aa 5-21
ATOMS2
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. 
 
ATOMS3
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. 
 
ATOMS4
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. 
 
ATOMS5
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. 
 
ATOMS6
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. 
 
ATOMS7
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. 
 
ATOMS8
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. 
 
ATOMS9
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. 
 
ATOMS10
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. 
 
ATOMS11
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. 
 
ATOMS12
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. 
 
ATOMS13
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. 
 
ATOMS14
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. 
 
ATOMS15
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. 
 
ATOMS16
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. 
 
ATOMS17
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. 
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab1
... ALPHABETA

ALPHABETA
Calculate the alpha beta CV More details
 ...
ATOMS1
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. 
 
REFERENCE
the reference values for each of the torsional angles
=-0.78540  # for psi alphahelix app -45 deg CV3 alpha aa 28-43
ATOMS2
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. 
 
ATOMS3
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. 
 
ATOMS4
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. 
 
ATOMS5
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. 
 
ATOMS6
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. 
 
ATOMS7
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. 
 
ATOMS8
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. 
 
ATOMS9
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. 
 
ATOMS10
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. 
ATOMS11
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. 
 
ATOMS12
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. 
ATOMS13
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. 
ATOMS14
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. 
ATOMS15
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. 
ATOMS16
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. 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab2
... ALPHABETA

ALPHABETA
Calculate the alpha beta CV More details
 ...
ATOMS1
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. 
 
REFERENCE
the reference values for each of the torsional angles
=-0.78540  # for psi alphahelix app -45 deg CV4 alpha aa 45-58
ATOMS2
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. 
 
ATOMS3
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. 
 
ATOMS4
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. 
 
ATOMS5
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. 
 
ATOMS6
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. 
ATOMS7
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. 
ATOMS8
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. 
ATOMS9
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. 
 
ATOMS10
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. 
 
ATOMS11
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. 
 
ATOMS12
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. 
ATOMS13
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. 
 
ATOMS14
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. 
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab3
... ALPHABETA

#walls
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
=rg_ca 
AT
the positions of the wall
=0.8 
KAPPA
the force constant for the wall
=1000.0
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
=rg_ca 
AT
the positions of the wall
=3.5 
KAPPA
the force constant for the wall
=1000.0

#metaD-wte
metad: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rg_ca,ab1,ab2,ab3 
PACE
the frequency for hill addition
=1000 
HEIGHT
the heights of the Gaussian hills
=0.5 
SIGMA
the widths of the Gaussian hills
=0.2,1,1,1 
FILE
 a file in which the list of added hills is stored
=HILLS 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298.00

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rg_ca,ab1,ab2,ab3 
FILE
the name of the file on which to output these quantities
=colvar 
STRIDE
 the frequency with which the quantities of interest should be output
=1000