PLUMED-NEST

Project ID: plumID:23.000
Source: plumed_PT.9.dat
Originally used with PLUMED version: 2.3.1
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

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
STRIDE
 the frequency with which molecules are reassembled
=1 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-328

The WHOLEMOLECULES action with label  calculates somethingeneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details

wteThe METAD action with label wte calculates the following quantities:
 Quantity   
 Type   
 Description  
wte.bias
scalar
the instantaneous value of the bias potential: 
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
=2000 
HEIGHT
the heights of the Gaussian hills
=1.5 
SIGMA
the widths of the Gaussian hills
=600.0 
FILE
 a file in which the list of added hills is stored
=data/hills/HILLS_PTWTE 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=25.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=412.4 
GRID_MIN
the lower bounds for the grid
=-540477.6 
GRID_MAX
the upper bounds for the grid
=360318.4 

#monitor energy and 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 labels of the values that you would like to print to the file
=ene 
FILE
the name of the file on which to output these quantities
=data/colvar/COLVAR_PTWTE

CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 ...
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=15,315  
SWITCH1
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.744} 
WEIGHT1
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=16,314  
SWITCH2
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.621} 
WEIGHT2
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=16,315  
SWITCH3
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.539} 
WEIGHT3
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=16,318  
SWITCH4
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.553} 
WEIGHT4
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=16,319  
SWITCH5
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.721} 
WEIGHT5
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=17,284  
SWITCH6
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.733} 
WEIGHT6
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=17,312  
SWITCH7
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.743} 
WEIGHT7
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=17,314  
SWITCH8
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.536} 
WEIGHT8
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS9
the atoms involved in each of the contacts you wish to calculate
=17,315  
SWITCH9
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.408} 
WEIGHT9
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS10
the atoms involved in each of the contacts you wish to calculate
=17,318  
SWITCH10
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.528} 
WEIGHT10
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS11
the atoms involved in each of the contacts you wish to calculate
=17,319  
SWITCH11
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.722} 
WEIGHT11
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS12
the atoms involved in each of the contacts you wish to calculate
=18,314  
SWITCH12
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.564} 
WEIGHT12
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS13
the atoms involved in each of the contacts you wish to calculate
=18,315  
SWITCH13
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.551} 
WEIGHT13
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS14
the atoms involved in each of the contacts you wish to calculate
=18,318  
SWITCH14
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.436} 
WEIGHT14
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS15
the atoms involved in each of the contacts you wish to calculate
=18,319  
SWITCH15
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.565} 
WEIGHT15
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS16
the atoms involved in each of the contacts you wish to calculate
=18,320  
SWITCH16
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.565} 
WEIGHT16
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS17
the atoms involved in each of the contacts you wish to calculate
=20,314  
SWITCH17
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.736} 
WEIGHT17
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS18
the atoms involved in each of the contacts you wish to calculate
=20,318  
SWITCH18
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.577} 
WEIGHT18
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS19
the atoms involved in each of the contacts you wish to calculate
=20,319  
SWITCH19
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.650} 
WEIGHT19
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS20
the atoms involved in each of the contacts you wish to calculate
=20,320  
SWITCH20
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.589} 
WEIGHT20
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS21
the atoms involved in each of the contacts you wish to calculate
=21,314  
SWITCH21
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.747} 
WEIGHT21
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS22
the atoms involved in each of the contacts you wish to calculate
=21,318  
SWITCH22
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.560} 
WEIGHT22
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS23
the atoms involved in each of the contacts you wish to calculate
=21,319  
SWITCH23
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.569} 
WEIGHT23
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS24
the atoms involved in each of the contacts you wish to calculate
=21,320  
SWITCH24
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.462} 
WEIGHT24
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS25
the atoms involved in each of the contacts you wish to calculate
=49,284  
SWITCH25
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.745} 
WEIGHT25
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS26
the atoms involved in each of the contacts you wish to calculate
=49,315  
SWITCH26
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.737} 
WEIGHT26
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS27
the atoms involved in each of the contacts you wish to calculate
=49,318  
SWITCH27
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.703} 
WEIGHT27
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS28
the atoms involved in each of the contacts you wish to calculate
=50,250  
SWITCH28
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.713} 
WEIGHT28
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS29
the atoms involved in each of the contacts you wish to calculate
=50,283  
SWITCH29
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.618} 
WEIGHT29
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS30
the atoms involved in each of the contacts you wish to calculate
=50,284  
SWITCH30
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.538} 
WEIGHT30
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS31
the atoms involved in each of the contacts you wish to calculate
=50,287  
SWITCH31
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.553} 
WEIGHT31
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS32
the atoms involved in each of the contacts you wish to calculate
=50,288  
SWITCH32
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.720} 
WEIGHT32
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS33
the atoms involved in each of the contacts you wish to calculate
=50,314  
SWITCH33
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.622} 
WEIGHT33
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS34
the atoms involved in each of the contacts you wish to calculate
=50,315  
SWITCH34
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.579} 
WEIGHT34
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS35
the atoms involved in each of the contacts you wish to calculate
=50,318  
SWITCH35
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.602} 
WEIGHT35
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS36
the atoms involved in each of the contacts you wish to calculate
=50,319  
SWITCH36
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.730} 
WEIGHT36
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS37
the atoms involved in each of the contacts you wish to calculate
=51,249  
SWITCH37
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.713} 
WEIGHT37
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS38
the atoms involved in each of the contacts you wish to calculate
=51,250  
SWITCH38
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.628} 
WEIGHT38
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS39
the atoms involved in each of the contacts you wish to calculate
=51,251  
SWITCH39
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.736} 
WEIGHT39
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS40
the atoms involved in each of the contacts you wish to calculate
=51,281  
SWITCH40
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.742} 
WEIGHT40
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS41
the atoms involved in each of the contacts you wish to calculate
=51,283  
SWITCH41
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.534} 
WEIGHT41
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS42
the atoms involved in each of the contacts you wish to calculate
=51,284  
SWITCH42
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.408} 
WEIGHT42
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS43
the atoms involved in each of the contacts you wish to calculate
=51,287  
SWITCH43
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.529} 
WEIGHT43
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS44
the atoms involved in each of the contacts you wish to calculate
=51,288  
SWITCH44
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.723} 
WEIGHT44
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS45
the atoms involved in each of the contacts you wish to calculate
=51,312  
SWITCH45
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.742} 
WEIGHT45
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS46
the atoms involved in each of the contacts you wish to calculate
=51,314  
SWITCH46
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.592} 
WEIGHT46
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS47
the atoms involved in each of the contacts you wish to calculate
=51,315  
SWITCH47
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.495} 
WEIGHT47
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS48
the atoms involved in each of the contacts you wish to calculate
=51,318  
SWITCH48
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.623} 
WEIGHT48
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS49
the atoms involved in each of the contacts you wish to calculate
=52,250  
SWITCH49
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.737} 
WEIGHT49
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS50
the atoms involved in each of the contacts you wish to calculate
=52,251  
SWITCH50
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.689} 
WEIGHT50
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS51
the atoms involved in each of the contacts you wish to calculate
=52,283  
SWITCH51
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.563} 
WEIGHT51
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS52
the atoms involved in each of the contacts you wish to calculate
=52,284  
SWITCH52
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.552} 
WEIGHT52
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS53
the atoms involved in each of the contacts you wish to calculate
=52,287  
SWITCH53
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.437} 
WEIGHT53
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS54
the atoms involved in each of the contacts you wish to calculate
=52,288  
SWITCH54
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.567} 
WEIGHT54
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS55
the atoms involved in each of the contacts you wish to calculate
=52,289  
SWITCH55
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.566} 
WEIGHT55
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS56
the atoms involved in each of the contacts you wish to calculate
=52,309  
SWITCH56
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.738} 
WEIGHT56
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS57
the atoms involved in each of the contacts you wish to calculate
=52,312  
SWITCH57
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.695} 
WEIGHT57
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS58
the atoms involved in each of the contacts you wish to calculate
=52,314  
SWITCH58
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.589} 
WEIGHT58
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS59
the atoms involved in each of the contacts you wish to calculate
=52,315  
SWITCH59
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.606} 
WEIGHT59
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS60
the atoms involved in each of the contacts you wish to calculate
=52,318  
SWITCH60
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.564} 
WEIGHT60
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS61
the atoms involved in each of the contacts you wish to calculate
=52,319  
SWITCH61
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.645} 
WEIGHT61
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS62
the atoms involved in each of the contacts you wish to calculate
=52,320  
SWITCH62
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.709} 
WEIGHT62
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS63
the atoms involved in each of the contacts you wish to calculate
=54,283  
SWITCH63
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.734} 
WEIGHT63
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS64
the atoms involved in each of the contacts you wish to calculate
=54,284  
SWITCH64
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.749} 
WEIGHT64
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS65
the atoms involved in each of the contacts you wish to calculate
=54,287  
SWITCH65
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.575} 
WEIGHT65
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS66
the atoms involved in each of the contacts you wish to calculate
=54,288  
SWITCH66
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.649} 
WEIGHT66
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS67
the atoms involved in each of the contacts you wish to calculate
=54,289  
SWITCH67
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.589} 
WEIGHT67
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS68
the atoms involved in each of the contacts you wish to calculate
=54,314  
SWITCH68
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.710} 
WEIGHT68
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS69
the atoms involved in each of the contacts you wish to calculate
=54,318  
SWITCH69
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.639} 
WEIGHT69
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS70
the atoms involved in each of the contacts you wish to calculate
=54,319  
SWITCH70
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.662} 
WEIGHT70
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS71
the atoms involved in each of the contacts you wish to calculate
=54,320  
SWITCH71
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.680} 
WEIGHT71
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS72
the atoms involved in each of the contacts you wish to calculate
=55,254  
SWITCH72
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.729} 
WEIGHT72
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS73
the atoms involved in each of the contacts you wish to calculate
=55,283  
SWITCH73
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.746} 
WEIGHT73
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS74
the atoms involved in each of the contacts you wish to calculate
=55,287  
SWITCH74
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.560} 
WEIGHT74
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS75
the atoms involved in each of the contacts you wish to calculate
=55,288  
SWITCH75
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.569} 
WEIGHT75
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS76
the atoms involved in each of the contacts you wish to calculate
=55,289  
SWITCH76
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.462} 
WEIGHT76
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS77
the atoms involved in each of the contacts you wish to calculate
=55,309  
SWITCH77
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.704} 
WEIGHT77
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS78
the atoms involved in each of the contacts you wish to calculate
=55,314  
SWITCH78
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.749} 
WEIGHT78
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS79
the atoms involved in each of the contacts you wish to calculate
=55,318  
SWITCH79
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.689} 
WEIGHT79
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS80
the atoms involved in each of the contacts you wish to calculate
=55,319  
SWITCH80
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.664} 
WEIGHT80
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS81
the atoms involved in each of the contacts you wish to calculate
=55,320  
SWITCH81
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.686} 
WEIGHT81
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS82
the atoms involved in each of the contacts you wish to calculate
=58,318  
SWITCH82
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.739} 
WEIGHT82
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS83
the atoms involved in each of the contacts you wish to calculate
=58,320  
SWITCH83
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.730} 
WEIGHT83
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS84
the atoms involved in each of the contacts you wish to calculate
=82,250  
SWITCH84
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.741} 
WEIGHT84
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS85
the atoms involved in each of the contacts you wish to calculate
=84,249  
SWITCH85
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.619} 
WEIGHT85
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS86
the atoms involved in each of the contacts you wish to calculate
=84,250  
SWITCH86
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.534} 
WEIGHT86
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS87
the atoms involved in each of the contacts you wish to calculate
=84,251  
SWITCH87
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.564} 
WEIGHT87
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS88
the atoms involved in each of the contacts you wish to calculate
=84,253  
SWITCH88
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.736} 
WEIGHT88
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS89
the atoms involved in each of the contacts you wish to calculate
=84,254  
SWITCH89
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.747} 
WEIGHT89
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS90
the atoms involved in each of the contacts you wish to calculate
=84,284  
SWITCH90
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.717} 
WEIGHT90
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS91
the atoms involved in each of the contacts you wish to calculate
=84,287  
SWITCH91
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.732} 
WEIGHT91
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS92
the atoms involved in each of the contacts you wish to calculate
=85,248  
SWITCH92
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.746} 
WEIGHT92
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS93
the atoms involved in each of the contacts you wish to calculate
=85,249  
SWITCH93
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.538} 
WEIGHT93
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS94
the atoms involved in each of the contacts you wish to calculate
=85,250  
SWITCH94
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.408} 
WEIGHT94
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS95
the atoms involved in each of the contacts you wish to calculate
=85,251  
SWITCH95
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.551} 
WEIGHT95
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS96
the atoms involved in each of the contacts you wish to calculate
=85,283  
SWITCH96
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.717} 
WEIGHT96
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS97
the atoms involved in each of the contacts you wish to calculate
=85,284  
SWITCH97
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.610} 
WEIGHT97
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS98
the atoms involved in each of the contacts you wish to calculate
=85,287  
SWITCH98
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.716} 
WEIGHT98
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS99
the atoms involved in each of the contacts you wish to calculate
=88,249  
SWITCH99
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.551} 
WEIGHT99
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS100
the atoms involved in each of the contacts you wish to calculate
=88,250  
SWITCH100
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.527} 
WEIGHT100
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS101
the atoms involved in each of the contacts you wish to calculate
=88,251  
SWITCH101
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.435} 
WEIGHT101
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS102
the atoms involved in each of the contacts you wish to calculate
=88,253  
SWITCH102
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.575} 
WEIGHT102
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS103
the atoms involved in each of the contacts you wish to calculate
=88,254  
SWITCH103
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.560} 
WEIGHT103
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS104
the atoms involved in each of the contacts you wish to calculate
=88,283  
SWITCH104
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.731} 
WEIGHT104
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS105
the atoms involved in each of the contacts you wish to calculate
=88,284  
SWITCH105
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.715} 
WEIGHT105
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS106
the atoms involved in each of the contacts you wish to calculate
=88,287  
SWITCH106
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.664} 
WEIGHT106
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS107
the atoms involved in each of the contacts you wish to calculate
=89,249  
SWITCH107
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.720} 
WEIGHT107
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS108
the atoms involved in each of the contacts you wish to calculate
=89,250  
SWITCH108
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.722} 
WEIGHT108
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS109
the atoms involved in each of the contacts you wish to calculate
=89,251  
SWITCH109
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.566} 
WEIGHT109
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS110
the atoms involved in each of the contacts you wish to calculate
=89,253  
SWITCH110
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.650} 
WEIGHT110
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS111
the atoms involved in each of the contacts you wish to calculate
=89,254  
SWITCH111
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.570} 
WEIGHT111
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS112
the atoms involved in each of the contacts you wish to calculate
=90,251  
SWITCH112
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.564} 
WEIGHT112
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS113
the atoms involved in each of the contacts you wish to calculate
=90,253  
SWITCH113
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.587} 
WEIGHT113
A weight value for a given contact, by default is 1
=0.00877192982
ATOMS114
the atoms involved in each of the contacts you wish to calculate
=90,254  
SWITCH114
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50 LAMBDA=1.0 REF=0.461} 
WEIGHT114
A weight value for a given contact, by default is 1
=0.00877192982
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cmapThe CONTACTMAP action with label cmap calculates the following quantities:
 Quantity   
 Type   
 Description  
cmap
scalar
the sum of all the switching function on all the distances
SUM
 calculate the sum of all the contacts in the input
NOPBC
 ignore the periodic boundary conditions when calculating distances
... CONTACTMAP

wtmThe METAD action with label wtm calculates the following quantities:
 Quantity   
 Type   
 Description  
wtm.bias
scalar
the instantaneous value of the bias potential: 
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
=cmap 
PACE
the frequency for hill addition
=1000 
HEIGHT
the heights of the Gaussian hills
=1.8 
SIGMA
the widths of the Gaussian hills
=0.01 
FILE
 a file in which the list of added hills is stored
=data/hills/hills 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=25 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=412.4 
INTERVAL
one dimensional lower and upper limits, outside the limits the system will not feel the biasing force
=0.01,0.99 
GRID_MIN
the lower bounds for the grid
=-0.05 
GRID_MAX
the upper bounds for the grid
=1.05

lwThe LOWER_WALLS action with label lw calculates the following quantities:
 Quantity   
 Type   
 Description  
lw.bias
scalar
the instantaneous value of the bias potential
lw.force2
scalar
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 arguments on which the bias is acting
=cmap 
AT
the positions of the wall
=0.01 
KAPPA
the force constant for the wall
=75000
uwThe UPPER_WALLS action with label uw calculates the following quantities:
 Quantity   
 Type   
 Description  
uw.bias
scalar
the instantaneous value of the bias potential
uw.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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
=cmap 
AT
the positions of the wall
=0.99 
KAPPA
the force constant for the wall
=75000

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
ARG
the labels of the values that you would like to print to the file
=cmap,wtm.bias,lw.bias,uw.bias 
FILE
the name of the file on which to output these quantities
=data/colvar/colvar