PLUMED-NEST

Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV4/plumed.3.dat
Originally used with PLUMED version: 2.5.2
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

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
=Protein.pdb 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=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
=1-709

RANDOM_EXCHANGES
Set random pattern for exchanges. More details

DIHCOR
Measures the degree of similarity between dihedral angles. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cv4
ATOMS1
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. 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. 
,
@psi-3
the four atoms that are required to calculate the psi 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
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. 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. 
ATOMS4
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. 
,
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
ATOMS5
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. 
,
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
ATOMS6
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. 
,
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
ATOMS7
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. 
,
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
ATOMS8
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. 
,
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
ATOMS9
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. 
,
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
ATOMS10
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. 
,
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
ATOMS11
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. 
,
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
ATOMS12
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. 
,
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
ATOMS13
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. 
,
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
ATOMS14
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. 
,
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
ATOMS15
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. 
,
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
ATOMS16
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. 
,
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
ATOMS17
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. 
,
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
ATOMS18
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. 
,
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
ATOMS19
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
,
@psi-20
the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
ATOMS20
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-20
the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
,
@psi-21
the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
ATOMS21
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-21
the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
,
@psi-22
the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
ATOMS22
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-22
the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
,
@psi-23
the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
ATOMS23
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-23
the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
,
@psi-24
the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
ATOMS24
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-24
the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
,
@psi-25
the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
ATOMS25
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-25
the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
,
@psi-26
the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
ATOMS26
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-26
the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
,
@psi-27
the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
ATOMS27
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-27
the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
,
@psi-28
the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
ATOMS28
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-28
the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
,
@psi-29
the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
ATOMS29
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-29
the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
,
@psi-30
the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
ATOMS30
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-30
the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
,
@psi-31
the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
ATOMS31
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-31
the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
,
@psi-32
the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
ATOMS32
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-32
the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
,
@psi-33
the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
ATOMS33
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-33
the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
,
@psi-34
the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
ATOMS34
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-34
the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
,
@psi-35
the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
ATOMS35
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-35
the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
,
@psi-36
the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
ATOMS36
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-36
the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
,
@psi-37
the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
ATOMS37
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-37
the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
,
@psi-38
the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
ATOMS38
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-38
the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
,
@psi-39
the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
ATOMS39
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-39
the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
,
@psi-40
the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
ATOMS40
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-40
the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
,
@psi-41
the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
ATOMS41
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-41
the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
,
@psi-42
the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information. 
ATOMS42
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-42
the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information. 
,
@psi-43
the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information. 
ATOMS43
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-43
the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information. 
,
@psi-44
the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information. 
ATOMS44
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-44
the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information. 
,
@psi-45
the four atoms that are required to calculate the psi dihedral for residue 45. Click here for more information. 
... DIHCOR

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
=cv4 
HEIGHT
the heights of the Gaussian hills
=0.3 
SIGMA
the widths of the Gaussian hills
=1.0 
PACE
the frequency for hill addition
=2500 
FILE
 a file in which the list of added hills is stored
=HILLS 
GRID_MIN
the lower bounds for the grid
=0.0 
GRID_MAX
the upper bounds for the grid
=44.0 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.1

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialuwall: 
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
=cv4 
AT
the positions of the wall
=40.0 
KAPPA
the force constant for the wall
=30.0
lwall: 
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
=cv4 
AT
the positions of the wall
=10.0 
KAPPA
the force constant for the wall
=30.0

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
=cv4,metad.bias,uwall.bias,lwall.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
#PRINT FILE=COLVAR ARG=cv4,metad.bias STRIDE=10