PLUMED-NEST

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

#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 input for this action is the scalar output from one or more other actions
=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
The METAD action with label ened calculates the following quantities:
 Quantity   
 Description  
ened.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=5000 
ARG
the input for this action is the scalar output from one or more other actions
=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. 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

The COORDINATION action with label cv2 calculates a scalar quantitycg: 
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. 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

The COORDINATION action with label cv3 calculates a scalar quantityo1: 
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. 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

The COORDINATION action with label cv4 calculates a scalar quantity
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
=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. 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 
The ALPHARMSD action with label cv6 calculates the following quantities:
 Quantity   
 Description  
cv6.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
cv6.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdcv7: 
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
=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
The ANTIBETARMSD action with label cv7 calculates the following quantities:
 Quantity   
 Description  
cv7.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
cv7.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdcv8: 
PARABETARMSD
Probe the parallel 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
=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

The PARABETARMSD action with label cv8 calculates the following quantities:
 Quantity   
 Description  
cv8.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
cv8.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdmetad: 
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
=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
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor $c(t)$
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 input for this action is the scalar output from one or more other actions
=cv2,cv3,cv4,cv5,cv6,cv7,cv8,rg,as,ka,metad.rbias