PLUMED-NEST

Project ID: plumID:23.045
Source: Path-CVs_MetaD/neca-bound/plumed.dat
Originally used with PLUMED version: 2.7.1
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

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
=FApo.pdb
The MOLINFO action with label  calculates somethingp: 
PATHMSD
This Colvar calculates path collective variables. More details
 
REFERENCE
the pdb is needed to provide the various milestones
=path_rmsd.pdb  
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=122.00
The PATHMSD action with label p calculates the following quantities:
 Quantity   
 Description  
p.sss
the position on the path
p.zzz
the distance from the pathd1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1458,3468
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3080,3468
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsH6: 
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
=220-252
The ALPHARMSD action with label H6 calculates the following quantities:
 Quantity   
 Description  
H6.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
H6.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdH5: 
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
=198-209

The ALPHARMSD action with label H5 calculates the following quantities:
 Quantity   
 Description  
H5.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
H5.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=path_cmap.dat
# The command:
# INCLUDE FILE=path_cmap.dat
# ensures PLUMED loads the contents of the file called path_cmap.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label path_cmap.dat calculates something
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
=3468,3080   
REFERENCE1
A reference value for a given contact, by default is 0
=0.97915123  
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=3468,1458   
REFERENCE2
A reference value for a given contact, by default is 0
=0.00041408  
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=3468,1438   
REFERENCE3
A reference value for a given contact, by default is 0
=0.02647680  
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1458,1438   
REFERENCE4
A reference value for a given contact, by default is 0
=0.08877594  
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=3566,2951   
REFERENCE5
A reference value for a given contact, by default is 0
=0.42785568  
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=3566,1387   
REFERENCE6
A reference value for a given contact, by default is 0
=0.10367204  
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=4418,2936   
REFERENCE7
A reference value for a given contact, by default is 0
=0.98727453  
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=4418,625    
REFERENCE8
A reference value for a given contact, by default is 0
=0.14748926  
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.67 NN=12 MM=24}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c1
CMDIST
 calculate the distance with respect to the provided reference contact map
... CONTACTMAP


The CONTACTMAP action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.contact
By not using SUM or CMDIST each contact will be stored in a component
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
=3468,3080   
REFERENCE1
A reference value for a given contact, by default is 0
=0.99076543  
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=3468,1458   
REFERENCE2
A reference value for a given contact, by default is 0
=0.00120232  
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=3468,1438   
REFERENCE3
A reference value for a given contact, by default is 0
=0.07366488  
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1458,1438   
REFERENCE4
A reference value for a given contact, by default is 0
=0.79523553  
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=3566,2951   
REFERENCE5
A reference value for a given contact, by default is 0
=0.28660977  
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=3566,1387   
REFERENCE6
A reference value for a given contact, by default is 0
=0.33348235  
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=4418,2936   
REFERENCE7
A reference value for a given contact, by default is 0
=0.96457138  
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=4418,625    
REFERENCE8
A reference value for a given contact, by default is 0
=0.12877288  
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.67 NN=12 MM=24}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c2
CMDIST
 calculate the distance with respect to the provided reference contact map
... CONTACTMAP


The CONTACTMAP action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.contact
By not using SUM or CMDIST each contact will be stored in a component
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
=3468,3080   
REFERENCE1
A reference value for a given contact, by default is 0
=0.97985636  
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=3468,1458   
REFERENCE2
A reference value for a given contact, by default is 0
=0.00298822  
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=3468,1438   
REFERENCE3
A reference value for a given contact, by default is 0
=0.32581507  
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1458,1438   
REFERENCE4
A reference value for a given contact, by default is 0
=0.97691480  
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=3566,2951   
REFERENCE5
A reference value for a given contact, by default is 0
=0.64179803  
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=3566,1387   
REFERENCE6
A reference value for a given contact, by default is 0
=0.39343434  
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=4418,2936   
REFERENCE7
A reference value for a given contact, by default is 0
=0.80857049  
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=4418,625    
REFERENCE8
A reference value for a given contact, by default is 0
=0.98023826  
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.67 NN=12 MM=24}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c3
CMDIST
 calculate the distance with respect to the provided reference contact map
... CONTACTMAP


The CONTACTMAP action with label c3 calculates the following quantities:
 Quantity   
 Description  
c3.contact
By not using SUM or CMDIST each contact will be stored in a component
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
=3468,3080   
REFERENCE1
A reference value for a given contact, by default is 0
=0.98302451  
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=3468,1458   
REFERENCE2
A reference value for a given contact, by default is 0
=0.00222719  
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=3468,1438   
REFERENCE3
A reference value for a given contact, by default is 0
=0.28721980  
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1458,1438   
REFERENCE4
A reference value for a given contact, by default is 0
=0.97341515  
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=3566,2951   
REFERENCE5
A reference value for a given contact, by default is 0
=0.39377719  
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=3566,1387   
REFERENCE6
A reference value for a given contact, by default is 0
=0.58032321  
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=4418,2936   
REFERENCE7
A reference value for a given contact, by default is 0
=0.10151712  
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=4418,625    
REFERENCE8
A reference value for a given contact, by default is 0
=0.99945112  
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.67 NN=12 MM=24}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c4
CMDIST
 calculate the distance with respect to the provided reference contact map
... CONTACTMAP

The CONTACTMAP action with label c4 calculates the following quantities:
 Quantity   
 Description  
c4.contact
By not using SUM or CMDIST each contact will be stored in a component
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
=3468,3080   
REFERENCE1
A reference value for a given contact, by default is 0
=0.37447568  
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=3468,1458   
REFERENCE2
A reference value for a given contact, by default is 0
=0.00700306  
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=3468,1438   
REFERENCE3
A reference value for a given contact, by default is 0
=0.47787638  
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1458,1438   
REFERENCE4
A reference value for a given contact, by default is 0
=0.97674738  
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=3566,2951   
REFERENCE5
A reference value for a given contact, by default is 0
=0.03917644  
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=3566,1387   
REFERENCE6
A reference value for a given contact, by default is 0
=0.99881752  
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=4418,2936   
REFERENCE7
A reference value for a given contact, by default is 0
=0.00122655  
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=4418,625    
REFERENCE8
A reference value for a given contact, by default is 0
=0.99974666  
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.67 NN=12 MM=24}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c5
CMDIST
 calculate the distance with respect to the provided reference contact map
... CONTACTMAP

The CONTACTMAP action with label c5 calculates the following quantities:
 Quantity   
 Description  
c5.contact
By not using SUM or CMDIST each contact will be stored in a component
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
=3468,3080   
REFERENCE1
A reference value for a given contact, by default is 0
=0.00478415  
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=3468,1458   
REFERENCE2
A reference value for a given contact, by default is 0
=0.37643526  
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=3468,1438   
REFERENCE3
A reference value for a given contact, by default is 0
=0.96181240  
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1458,1438   
REFERENCE4
A reference value for a given contact, by default is 0
=0.96500778  
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=3566,2951   
REFERENCE5
A reference value for a given contact, by default is 0
=0.16431360  
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=3566,1387   
REFERENCE6
A reference value for a given contact, by default is 0
=0.98327651  
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=4418,2936   
REFERENCE7
A reference value for a given contact, by default is 0
=0.28874741  
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=4418,625    
REFERENCE8
A reference value for a given contact, by default is 0
=0.96352033  
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.67 NN=12 MM=24}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c6
CMDIST
 calculate the distance with respect to the provided reference contact map
... CONTACTMAP


The CONTACTMAP action with label c6 calculates the following quantities:
 Quantity   
 Description  
c6.contact
By not using SUM or CMDIST each contact will be stored in a component
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
=3468,3080   
REFERENCE1
A reference value for a given contact, by default is 0
=0.00064458  
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=3468,1458   
REFERENCE2
A reference value for a given contact, by default is 0
=0.93811079  
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=3468,1438   
REFERENCE3
A reference value for a given contact, by default is 0
=0.99043541  
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1458,1438   
REFERENCE4
A reference value for a given contact, by default is 0
=0.96998468  
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=3566,2951   
REFERENCE5
A reference value for a given contact, by default is 0
=0.03311838  
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=3566,1387   
REFERENCE6
A reference value for a given contact, by default is 0
=0.99966434  
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=4418,2936   
REFERENCE7
A reference value for a given contact, by default is 0
=0.06060704  
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=4418,625    
REFERENCE8
A reference value for a given contact, by default is 0
=0.99816484  
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.67 NN=12 MM=24}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c7
CMDIST
 calculate the distance with respect to the provided reference contact map
... CONTACTMAP

# --- End of included input --- The CONTACTMAP action with label c7 calculates the following quantities:
 Quantity   
 Description  
c7.contact
By not using SUM or CMDIST each contact will be stored in a componentp1: 
FUNCPATHMSD
This function calculates path collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=c1,c2,c3,c4,c5,c6,c7  
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=3.634


The FUNCPATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.s
the position on the path
p1.z
the distance from the pathmeta: 
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
=p.sss,p1.s 
SIGMA
the widths of the Gaussian hills
=0.1,0.03  
HEIGHT
the heights of the Gaussian hills
=4 
PACE
the frequency for hill addition
=1000 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
GRID_MIN
the lower bounds for the grid
=1,1 
GRID_MAX
the upper bounds for the grid
=12,7 
GRID_WFILE
the file on which to write the grid
=GRID_W  
GRID_WSTRIDE
write the grid to a file every N steps
=2500000

#Helicity Wall
The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.bias
the instantaneous value of the bias potentiallwall: 
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
=H6 
AT
the positions of the wall
=24.8 
KAPPA
the force constant for the wall
=1500.0

#TM3-TM5 Distances
The LOWER_WALLS action with label lwall calculates somethingd3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1519,3047
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1469,2989
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1414,2909
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsuwall1: 
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
=d3  
AT
the positions of the wall
=0.75 
KAPPA
the force constant for the wall
=100.000
The UPPER_WALLS action with label uwall1 calculates somethinguwall2: 
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
=d4  
AT
the positions of the wall
=0.625 
KAPPA
the force constant for the wall
=100.000
The UPPER_WALLS action with label uwall2 calculates somethinguwall3: 
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
=d5  
AT
the positions of the wall
=0.7 
KAPPA
the force constant for the wall
=100.000
The UPPER_WALLS action with label uwall3 calculates somethinguwallpz: 
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
=p1.z 
AT
the positions of the wall
=0.05 
KAPPA
the force constant for the wall
=1000.0

The UPPER_WALLS action with label uwallpz calculates somethingd6: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2936,4418
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsuw: 
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
=d6 
AT
the positions of the wall
=0.65 
KAPPA
the force constant for the wall
=00.000
The UPPER_WALLS action with label uw calculates somethingd7: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3468,3332
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomslw: 
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
=d7 
AT
the positions of the wall
=0.7 
KAPPA
the force constant for the wall
=100.00
The LOWER_WALLS action with label lw calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=COLVAR