Project ID: plumID:21.036
Source: DHH1N_sampling/PTMetaD-WTE/plumed_CVs_PTMetaD-WTE.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
tested onv2.10
tested onmaster
#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
ene:
ENERGY
Calculate the total potential energy of the simulation box. More details
ened:
METAD
Used to performed metadynamics on one or more collective variables. More details
ARG
the labels of the scalars on which the bias will act
=ene
PACE
the frequency for hill addition
=500000000
HEIGHT
the heights of the Gaussian hills
=1.2
SIGMA
the widths of the Gaussian hills
=2000.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
BIASFACTOR
use well tempered metadynamics and use this bias factor
=12
FILE
a file in which the list of added hills is stored
=HILLS
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=5000
ARG
the labels of the values that you would like to print to the file
=ene,ened.bias
FILE
the name of the file on which to output these quantities
=COLVAR_ENE
ca:
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
=5,12,23,42,56,70,84,104,118,132,146,160,174,185,199,213,225,244,256,280,292,316,338,352,362,381,395,416,428,450,472,484,498,524,536,553,567,579,591,607,626,640,654,676,683,697 cv2:
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
GROUPA
First list of atoms
=ca
NN
The n parameter of the switching function
=8
MM
The m parameter of the switching function; 0 implies 2*NN
=10
R_0
The r_0 parameter of the switching function
=0.65
NOPBC
ignore the periodic boundary conditions when calculating distances
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=5.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5

cg:
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
=27,31,47,61,75,89,109,124,137,151,165,190,205,218,230,249,261,285,297,321,344,367,386,399,403,421,433,455,477,490,503,529,541,559,572,584,595,599,612,631,646,659,688,703 cv3:
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
GROUPA
First list of atoms
=cg
R_0
The r_0 parameter of the switching function
=0.5
NN
The n parameter of the switching function
=8
MM
The m parameter of the switching function; 0 implies 2*NN
=10
NOPBC
ignore the periodic boundary conditions when calculating distances
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=4.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5

o1:
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
=20,39,53,67,81,101,115,129,143,157,171,182,196,210,222,241,253,277,289,313,335,349,359,378,392,425,447,469,481,495,533,550,564,576,588,604,623,637,651,673,680,694 h1:
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
=11,22,41,55,69,83,103,117,131,145,159,173,184,198,212,224,243,255,279,291,315,337,351,361,380,394,427,449,471,483,497,535,552,566,578,590,606,625,639,653,675,682 cv4:
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
GROUPA
First list of atoms
=h1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=o1
R_0
The r_0 parameter of the switching function
=0.20
NN
The n parameter of the switching function
=8
MM
The m parameter of the switching function; 0 implies 2*NN
=10
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
NOPBC
ignore the periodic boundary conditions when calculating distances
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=3.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5

DIHCOR
Measures the degree of similarity between dihedral angles. This action is a shortcut. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cv5
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

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
=1-709
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rg
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
=ASPHERICITY
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1-709
LABEL
a label for the action so that its output can be referenced in the input to other actions
=as
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
=KAPPA2
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1-709
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ka
cv6:
ALPHARMSD
Probe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=1-45
TYPE
the manner in which RMSD alignment is performed
=DRMSD
R_0
The r_0 parameter of the switching function
=0.08
NN
The n parameter of the switching function
=2
MM
The m parameter of the switching function
=4
cv7:
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=1-45
TYPE
the manner in which RMSD alignment is performed
=DRMSD
R_0
The r_0 parameter of the switching function
=0.08
NN
The n parameter of the switching function
=8
MM
The m parameter of the switching function
=12
cv8:
PARABETARMSD
Probe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=1-45
TYPE
the manner in which RMSD alignment is performed
=DRMSD
NN
The n parameter of the switching function
=8
MM
The m parameter of the switching function
=12
R_0
The r_0 parameter of the switching function
=0.08

metad:
METAD
Used to performed metadynamics on one or more collective variables. More details
ARG
the labels of the scalars on which the bias will act
=cv2,cv3
PACE
the frequency for hill addition
=500
HEIGHT
the heights of the Gaussian hills
=1.2
SIGMA
the widths of the Gaussian hills
=1.0,1.0
FILE
a file in which the list of added hills is stored
=HILLS_PTWTE
BIASFACTOR
use well tempered metadynamics and use this bias factor
=12
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
GRID_MIN
the lower bounds for the grid
=100,50
GRID_MAX
the upper bounds for the grid
=500,300
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.2,0.2
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
RCT_USTRIDE
the update stride for calculating the c(t) reweighting factor
=10
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=5000
FILE
the name of the file on which to output these quantities
=COLVAR_PTWTE_cv2
ARG
the labels of the values that you would like to print to the file
=cv2,cv3,cv4,cv5,cv6,cv7,cv8,rg,as,ka,metad.rbias