PLUMED-NEST

Project ID: plumID:22.024
Source: vhh/plumed.dat
Originally used with PLUMED version: 2.6
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
Activate restart. More details
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein 
STRUCTURE
a file in pdb format containing a reference structure
=template.pdb
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
=1-1909
# DEBUG DETAILED_TIMERS

# AB over backbone
ALPHABETA
Calculate the alpha beta CV More details
 ...
    
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@phi-98
the four atoms that are required to calculate the phi dihedral for residue 98. Click here for more information. 
 
REFERENCE
the reference values for each of the torsional angles
=pi
    
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=
@phi-99
the four atoms that are required to calculate the phi dihedral for residue 99. Click here for more information. 
    
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=
@phi-100
the four atoms that are required to calculate the phi dihedral for residue 100. Click here for more information. 
    
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=
@phi-101
the four atoms that are required to calculate the phi dihedral for residue 101. Click here for more information. 
    
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=
@phi-102
the four atoms that are required to calculate the phi dihedral for residue 102. Click here for more information. 
    
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=
@phi-103
the four atoms that are required to calculate the phi dihedral for residue 103. Click here for more information. 
    
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=
@phi-104
the four atoms that are required to calculate the phi dihedral for residue 104. Click here for more information. 
    
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=
@phi-105
the four atoms that are required to calculate the phi dihedral for residue 105. Click here for more information. 
    
ATOMS9
the atoms involved for each of the torsions you wish to calculate
=
@phi-106
the four atoms that are required to calculate the phi dihedral for residue 106. Click here for more information. 
    
ATOMS10
the atoms involved for each of the torsions you wish to calculate
=
@phi-107
the four atoms that are required to calculate the phi dihedral for residue 107. Click here for more information. 
    
ATOMS11
the atoms involved for each of the torsions you wish to calculate
=
@phi-108
the four atoms that are required to calculate the phi dihedral for residue 108. Click here for more information. 
    
ATOMS12
the atoms involved for each of the torsions you wish to calculate
=
@phi-109
the four atoms that are required to calculate the phi dihedral for residue 109. Click here for more information. 
    
ATOMS13
the atoms involved for each of the torsions you wish to calculate
=
@phi-110
the four atoms that are required to calculate the phi dihedral for residue 110. Click here for more information. 
    
ATOMS14
the atoms involved for each of the torsions you wish to calculate
=
@phi-111
the four atoms that are required to calculate the phi dihedral for residue 111. Click here for more information. 
    
ATOMS15
the atoms involved for each of the torsions you wish to calculate
=
@phi-112
the four atoms that are required to calculate the phi dihedral for residue 112. Click here for more information. 
    
ATOMS16
the atoms involved for each of the torsions you wish to calculate
=
@phi-113
the four atoms that are required to calculate the phi dihedral for residue 113. Click here for more information. 
    
ATOMS17
the atoms involved for each of the torsions you wish to calculate
=
@phi-114
the four atoms that are required to calculate the phi dihedral for residue 114. Click here for more information. 
    
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@phi-115
the four atoms that are required to calculate the phi dihedral for residue 115. Click here for more information. 
    
ATOMS19
the atoms involved for each of the torsions you wish to calculate
=
@phi-116
the four atoms that are required to calculate the phi dihedral for residue 116. Click here for more information. 
    
ATOMS20
the atoms involved for each of the torsions you wish to calculate
=
@phi-117
the four atoms that are required to calculate the phi dihedral for residue 117. Click here for more information. 
    
ATOMS21
the atoms involved for each of the torsions you wish to calculate
=
@phi-118
the four atoms that are required to calculate the phi dihedral for residue 118. Click here for more information. 
    
ATOMS22
the atoms involved for each of the torsions you wish to calculate
=
@phi-119
the four atoms that are required to calculate the phi dihedral for residue 119. Click here for more information. 
    
ATOMS23
the atoms involved for each of the torsions you wish to calculate
=
@phi-120
the four atoms that are required to calculate the phi dihedral for residue 120. Click here for more information. 
    
ATOMS24
the atoms involved for each of the torsions you wish to calculate
=
@phi-121
the four atoms that are required to calculate the phi dihedral for residue 121. Click here for more information. 
    
ATOMS25
the atoms involved for each of the torsions you wish to calculate
=
@psi-98
the four atoms that are required to calculate the psi dihedral for residue 98. Click here for more information. 
    
ATOMS26
the atoms involved for each of the torsions you wish to calculate
=
@psi-99
the four atoms that are required to calculate the psi dihedral for residue 99. Click here for more information. 
    
ATOMS27
the atoms involved for each of the torsions you wish to calculate
=
@psi-100
the four atoms that are required to calculate the psi dihedral for residue 100. Click here for more information. 
    
ATOMS28
the atoms involved for each of the torsions you wish to calculate
=
@psi-101
the four atoms that are required to calculate the psi dihedral for residue 101. Click here for more information. 
    
ATOMS29
the atoms involved for each of the torsions you wish to calculate
=
@psi-102
the four atoms that are required to calculate the psi dihedral for residue 102. Click here for more information. 
    
ATOMS30
the atoms involved for each of the torsions you wish to calculate
=
@psi-103
the four atoms that are required to calculate the psi dihedral for residue 103. Click here for more information. 
    
ATOMS31
the atoms involved for each of the torsions you wish to calculate
=
@psi-104
the four atoms that are required to calculate the psi dihedral for residue 104. Click here for more information. 
    
ATOMS32
the atoms involved for each of the torsions you wish to calculate
=
@psi-105
the four atoms that are required to calculate the psi dihedral for residue 105. Click here for more information. 
    
ATOMS33
the atoms involved for each of the torsions you wish to calculate
=
@psi-106
the four atoms that are required to calculate the psi dihedral for residue 106. Click here for more information. 
    
ATOMS34
the atoms involved for each of the torsions you wish to calculate
=
@psi-107
the four atoms that are required to calculate the psi dihedral for residue 107. Click here for more information. 
    
ATOMS35
the atoms involved for each of the torsions you wish to calculate
=
@psi-108
the four atoms that are required to calculate the psi dihedral for residue 108. Click here for more information. 
    
ATOMS36
the atoms involved for each of the torsions you wish to calculate
=
@psi-109
the four atoms that are required to calculate the psi dihedral for residue 109. Click here for more information. 
    
ATOMS37
the atoms involved for each of the torsions you wish to calculate
=
@psi-110
the four atoms that are required to calculate the psi dihedral for residue 110. Click here for more information. 
    
ATOMS38
the atoms involved for each of the torsions you wish to calculate
=
@psi-111
the four atoms that are required to calculate the psi dihedral for residue 111. Click here for more information. 
    
ATOMS39
the atoms involved for each of the torsions you wish to calculate
=
@psi-112
the four atoms that are required to calculate the psi dihedral for residue 112. Click here for more information. 
    
ATOMS40
the atoms involved for each of the torsions you wish to calculate
=
@psi-113
the four atoms that are required to calculate the psi dihedral for residue 113. Click here for more information. 
    
ATOMS41
the atoms involved for each of the torsions you wish to calculate
=
@psi-114
the four atoms that are required to calculate the psi dihedral for residue 114. Click here for more information. 
    
ATOMS42
the atoms involved for each of the torsions you wish to calculate
=
@psi-115
the four atoms that are required to calculate the psi dihedral for residue 115. Click here for more information. 
    
ATOMS43
the atoms involved for each of the torsions you wish to calculate
=
@psi-116
the four atoms that are required to calculate the psi dihedral for residue 116. Click here for more information. 
    
ATOMS44
the atoms involved for each of the torsions you wish to calculate
=
@psi-117
the four atoms that are required to calculate the psi dihedral for residue 117. Click here for more information. 
    
ATOMS45
the atoms involved for each of the torsions you wish to calculate
=
@psi-118
the four atoms that are required to calculate the psi dihedral for residue 118. Click here for more information. 
    
ATOMS46
the atoms involved for each of the torsions you wish to calculate
=
@psi-119
the four atoms that are required to calculate the psi dihedral for residue 119. Click here for more information. 
    
ATOMS47
the atoms involved for each of the torsions you wish to calculate
=
@psi-120
the four atoms that are required to calculate the psi dihedral for residue 120. Click here for more information. 
    
ATOMS48
the atoms involved for each of the torsions you wish to calculate
=
@psi-121
the four atoms that are required to calculate the psi dihedral for residue 121. Click here for more information. 
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=abbb
... ALPHABETA

# AB over sidechains
ALPHABETA
Calculate the alpha beta CV More details
 ...
    
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@chi1-99
the four atoms that are required to calculate the chi1 dihedral for residue 99. Click here for more information. 
 
REFERENCE
the reference values for each of the torsional angles
=pi
    
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=
@chi1-100
the four atoms that are required to calculate the chi1 dihedral for residue 100. Click here for more information. 
    
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=
@chi1-101
the four atoms that are required to calculate the chi1 dihedral for residue 101. Click here for more information. 
    
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=
@chi1-103
the four atoms that are required to calculate the chi1 dihedral for residue 103. Click here for more information. 
    
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=
@chi1-104
the four atoms that are required to calculate the chi1 dihedral for residue 104. Click here for more information. 
    
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=
@chi1-105
the four atoms that are required to calculate the chi1 dihedral for residue 105. Click here for more information. 
    
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=
@chi1-107
the four atoms that are required to calculate the chi1 dihedral for residue 107. Click here for more information. 
    
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=
@chi1-108
the four atoms that are required to calculate the chi1 dihedral for residue 108. Click here for more information. 
    
ATOMS9
the atoms involved for each of the torsions you wish to calculate
=
@chi1-109
the four atoms that are required to calculate the chi1 dihedral for residue 109. Click here for more information. 
    
ATOMS10
the atoms involved for each of the torsions you wish to calculate
=
@chi1-110
the four atoms that are required to calculate the chi1 dihedral for residue 110. Click here for more information. 
    
ATOMS11
the atoms involved for each of the torsions you wish to calculate
=
@chi1-111
the four atoms that are required to calculate the chi1 dihedral for residue 111. Click here for more information. 
    
ATOMS12
the atoms involved for each of the torsions you wish to calculate
=
@chi1-112
the four atoms that are required to calculate the chi1 dihedral for residue 112. Click here for more information. 
    
ATOMS13
the atoms involved for each of the torsions you wish to calculate
=
@chi1-113
the four atoms that are required to calculate the chi1 dihedral for residue 113. Click here for more information. 
    
ATOMS14
the atoms involved for each of the torsions you wish to calculate
=
@chi1-114
the four atoms that are required to calculate the chi1 dihedral for residue 114. Click here for more information. 
    
ATOMS15
the atoms involved for each of the torsions you wish to calculate
=
@chi1-115
the four atoms that are required to calculate the chi1 dihedral for residue 115. Click here for more information. 
    
ATOMS16
the atoms involved for each of the torsions you wish to calculate
=
@chi1-116
the four atoms that are required to calculate the chi1 dihedral for residue 116. Click here for more information. 
    
ATOMS17
the atoms involved for each of the torsions you wish to calculate
=
@chi1-117
the four atoms that are required to calculate the chi1 dihedral for residue 117. Click here for more information. 
    
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@chi1-118
the four atoms that are required to calculate the chi1 dihedral for residue 118. Click here for more information. 
    
ATOMS19
the atoms involved for each of the torsions you wish to calculate
=
@chi1-120
the four atoms that are required to calculate the chi1 dihedral for residue 120. Click here for more information. 
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=absc
... ALPHABETA

# Alpha-helix for CDR
helix: 
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
=98-121 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
LESS_THAN
calculate the number of a residue segments that are within a certain target distance of this secondary structure type
={RATIONAL R_0=0.08 NN=8 MM=12}

# Beta-sheet for CDR
The ALPHARMSD action with label helix calculates the following quantities:
 Quantity   
 Description  
helix.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
helix.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdanti: 
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
=98-121 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
LESS_THAN
calculate the number of a residue segments that are within a certain target distance of this secondary structure type
={RATIONAL R_0=0.08 NN=8 MM=12}

# Global CDR dihedral (Residues 98, 106, 112, 120)
The ANTIBETARMSD action with label anti calculates the following quantities:
 Quantity   
 Description  
anti.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdres1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1458,1459,1460,1461,1462,1463,1464,1465,1466,1467
res2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1569,1570,1571,1572,1573,1574,1575
res3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1658,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1669,1670,1671
res4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1786,1787,1788,1789,1790,1791,1792,1793,1794,1795,1796,1797,1798,1799,1800,1801,1802
dih: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=res1,res2,res3,res4

The TORSION action with label dih calculates a scalar quantity
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pbmetad
    
ARG
the input for this action is the scalar output from one or more other actions
=abbb,absc,helix.lessthan,anti.lessthan
    
PACE
the frequency for hill addition, one for all biases
=500 
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=24 
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
    
SIGMA
the widths of the Gaussian hills
=1.5,0.5,2.0,1.5
    
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS_abbb,HILLS_absc,HILLS_helix,HILLS_anti
    
GRID_MIN
the lower bounds for the grid
=-1,-1,-1,-1
    
GRID_MAX
the upper bounds for the grid
=50,20,100,100
    
GRID_WFILES
dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES
=GRID_abbb,GRID_absc,GRID_helix,GRID_anti
    #GRID_RFILES=GRID_abbb,GRID_absc,GRID_helix,GRID_anti
    
GRID_WSTRIDE
frequency for dumping the grid
=10000
... PBMETAD

The PBMETAD action with label pbmetad calculates the following quantities:
 Quantity   
 Description  
pbmetad.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
=500 
FILE
the name of the file on which to output these quantities
=BIAS 
ARG
the input for this action is the scalar output from one or more other actions
=abbb,absc,helix.lessthan,anti.lessthan,pbmetad.bias