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

The GYRATION action with label rg_ca calculates a scalar quantity
ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 ...
ATOMS1
the atoms involved in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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

The ALPHABETA action with label ab1 calculates a scalar quantity
ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 ...
ATOMS1
the atoms involved in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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

The ALPHABETA action with label ab2 calculates a scalar quantity
ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 ...
ATOMS1
the atoms involved in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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 in each of the alpha-beta variables 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
The ALPHABETA action with label ab3 calculates a scalar quantity
UPPER_WALLS
Defines a wall for the value of 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 
AT
the positions of the wall
=0.8 
KAPPA
the force constant for the wall
=1000.0
The UPPER_WALLS action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
.force2
the instantaneous value of the squared force due to this bias potential
LOWER_WALLS
Defines a wall for the value of 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 
AT
the positions of the wall
=3.5 
KAPPA
the force constant for the wall
=1000.0

#metaD-wte
The LOWER_WALLS action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
.force2
the instantaneous value of the squared force due to this bias potentialmetad: 
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