PLUMED-NEST

Project ID: plumID:21.045
Source: plumed.dat
Originally used with PLUMED version: 2.5.1
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

#########################
###   S-S DISTANCES   ###
###      and WALLS    ###
#########################

### CYS1-CYS2 ### 
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,10
### CYS1-CYS3 ### 
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,15
### CYS2-CYS3 ###
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,15

# Upper Walls distances
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
=d1,d2,d3 
	
AT
the positions of the wall
=0.6,0.6,0.6 
	
KAPPA
the force constant for the wall
=100000.0,100000.0,100000.0
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall-distThe UPPER_WALLS action with label uwall-dist calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall-dist.bias
scalar
the instantaneous value of the bias potential
uwall-dist.force2
scalar
the instantaneous value of the squared force due to this bias potential
... UPPER_WALLS

sum_distThe COMBINE action with label sum_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
sum_dist
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1,d2,d3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

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
=sum_dist 
    
AT
the positions of the wall
=0.9 
    
KAPPA
the force constant for the wall
=100000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall-sum_distThe LOWER_WALLS action with label lwall-sum_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall-sum_dist.bias
scalar
the instantaneous value of the bias potential
lwall-sum_dist.force2
scalar
the instantaneous value of the squared force due to this bias potential
... LOWER_WALLS

#########################
###  S-S COORDINATION ###
###     and WALLS     ###
#########################

### S1 Coord ###
c1The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=5  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10,15 
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20
c1: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=5  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10,15 
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20  
D_0
 The d_0 parameter of the switching function
=0.0
### S2 Coord ###
c2The COORDINATION action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5,15  
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20
c2: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5,15  
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20  
D_0
 The d_0 parameter of the switching function
=0.0
### S3 Coord ###
c3The COORDINATION action with label c3 calculates the following quantities:
 Quantity   
 Type   
 Description  
c3
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=15 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5,10  
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20
c3: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=15 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5,10  
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20  
D_0
 The d_0 parameter of the switching function
=0.0

### Sum of the three coordination nr. ###
### and lower walls on the sum of the ###
### coordination numbers to keep the  ###
### S-S distance below ~0.23 nm       ###
coord-sumThe COMBINE action with label coord-sum calculates the following quantities:
 Quantity   
 Type   
 Description  
coord-sum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=c1,c2,c3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
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
=coord-sum 
AT
the positions of the wall
=1.82 
KAPPA
the force constant for the wall
=20000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall-coordThe LOWER_WALLS action with label lwall-coord calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall-coord.bias
scalar
the instantaneous value of the bias potential
lwall-coord.force2
scalar
the instantaneous value of the squared force due to this bias potential

### Upper walls on each Coord nr. to ###
### avoid reaction to S-S-S species  ###
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
=c1,c2,c3
    
AT
the positions of the wall
=1.8,1.8,1.8
    
KAPPA
the force constant for the wall
=50000,50000,50000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall-coordThe UPPER_WALLS action with label uwall-coord calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall-coord.bias
scalar
the instantaneous value of the bias potential
uwall-coord.force2
scalar
the instantaneous value of the squared force due to this bias potential
... UPPER_WALLS

### Print dist+coord and wall-bias ###
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,c1,c2,c3,coord-sum,lwall-coord.bias,uwall-coord.bias,uwall-dist.bias,lwall-sum_dist.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=20 
FILE
the name of the file on which to output these quantities
=coord_s-s.dat

####################
### Coordination ###
### of CB-atoms  ###
####################
The PRINT action with label  calculates somethingcys1-coordThe COORDINATIONNUMBER action with label cys1-coord calculates the following quantities:
 Quantity   
 Type   
 Description  
cys1-coord
vector
the value calculated by this action
cys1-coord_mean
scalar
the mean of the colvars: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=2  
SPECIESB
this keyword is used for colvars such as the coordination number
=1,3,4    
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities
cys1-coord: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=2  
SPECIESB
this keyword is used for colvars such as the coordination number
=1,3,4    
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities
  
D_0
 The d_0 parameter of the switching function
=0.0
# PLUMED interprets the command:
# cys1-coord: COORDINATIONNUMBER SPECIESA=2  SPECIESB=1,3,4    R_0=0.130 NN=45 MM=90 MEAN
# as follows (Click the red comment above to revert to the short version of the input):
cys1-coord_grpThe GROUP action with label cys1-coord_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cys1-coord_grp
atoms
indices of atoms specified in GROUP: 
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
=2 
cys1-coord_matThe CONTACT_MATRIX action with label cys1-coord_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cys1-coord_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
R_0
The r_0 parameter of the switching function
=0.130 
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
cys1-coord_onesThe CONSTANT action with label cys1-coord_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cys1-coord_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=3
cys1-coordThe MATRIX_VECTOR_PRODUCT action with label cys1-coord calculates the following quantities:
 Quantity   
 Type   
 Description  
cys1-coord
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cys1-coord_mat,cys1-coord_ones 
cys1-coord_caverageThe MEAN action with label cys1-coord_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cys1-coord_caverage
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cys1-coord 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
cys1-coord_meanThe MEAN action with label cys1-coord_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
cys1-coord_mean
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cys1-coord 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- cys2-coordThe COORDINATIONNUMBER action with label cys2-coord calculates the following quantities:
 Quantity   
 Type   
 Description  
cys2-coord
vector
the value calculated by this action
cys2-coord_mean
scalar
the mean of the colvars: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=7  
SPECIESB
this keyword is used for colvars such as the coordination number
=6,8,9    
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities
cys2-coord: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=7  
SPECIESB
this keyword is used for colvars such as the coordination number
=6,8,9    
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities
  
D_0
 The d_0 parameter of the switching function
=0.0
# PLUMED interprets the command:
# cys2-coord: COORDINATIONNUMBER SPECIESA=7  SPECIESB=6,8,9    R_0=0.130 NN=45 MM=90 MEAN
# as follows (Click the red comment above to revert to the short version of the input):
cys2-coord_grpThe GROUP action with label cys2-coord_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cys2-coord_grp
atoms
indices of atoms specified in GROUP: 
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
=7 
cys2-coord_matThe CONTACT_MATRIX action with label cys2-coord_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cys2-coord_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
R_0
The r_0 parameter of the switching function
=0.130 
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
cys2-coord_onesThe CONSTANT action with label cys2-coord_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cys2-coord_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=3
cys2-coordThe MATRIX_VECTOR_PRODUCT action with label cys2-coord calculates the following quantities:
 Quantity   
 Type   
 Description  
cys2-coord
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cys2-coord_mat,cys2-coord_ones 
cys2-coord_caverageThe MEAN action with label cys2-coord_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cys2-coord_caverage
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cys2-coord 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
cys2-coord_meanThe MEAN action with label cys2-coord_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
cys2-coord_mean
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cys2-coord 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- cys3-coordThe COORDINATIONNUMBER action with label cys3-coord calculates the following quantities:
 Quantity   
 Type   
 Description  
cys3-coord
vector
the value calculated by this action
cys3-coord_mean
scalar
the mean of the colvars: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=12 
SPECIESB
this keyword is used for colvars such as the coordination number
=11,13,14 
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities
cys3-coord: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=12 
SPECIESB
this keyword is used for colvars such as the coordination number
=11,13,14 
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities
  
D_0
 The d_0 parameter of the switching function
=0.0
# PLUMED interprets the command:
# cys3-coord: COORDINATIONNUMBER SPECIESA=12 SPECIESB=11,13,14 R_0=0.130 NN=45 MM=90 MEAN
# as follows (Click the red comment above to revert to the short version of the input):
cys3-coord_grpThe GROUP action with label cys3-coord_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cys3-coord_grp
atoms
indices of atoms specified in GROUP: 
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
=12 
cys3-coord_matThe CONTACT_MATRIX action with label cys3-coord_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cys3-coord_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
R_0
The r_0 parameter of the switching function
=0.130 
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
cys3-coord_onesThe CONSTANT action with label cys3-coord_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cys3-coord_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=3
cys3-coordThe MATRIX_VECTOR_PRODUCT action with label cys3-coord calculates the following quantities:
 Quantity   
 Type   
 Description  
cys3-coord
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cys3-coord_mat,cys3-coord_ones 
cys3-coord_caverageThe MEAN action with label cys3-coord_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cys3-coord_caverage
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cys3-coord 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
cys3-coord_meanThe MEAN action with label cys3-coord_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
cys3-coord_mean
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cys3-coord 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
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
=cys1-coord.mean,cys2-coord.mean,cys3-coord.mean
    
AT
the positions of the wall
=2.5,2.5,2.5
    
KAPPA
the force constant for the wall
=50000,50000,50000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall-HBThe LOWER_WALLS action with label lwall-HB calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall-HB.bias
scalar
the instantaneous value of the bias potential
lwall-HB.force2
scalar
the instantaneous value of the squared force due to this bias potential
... LOWER_WALLS

####################
### Lower Walls  ###
###   S - HB     ###
####################

S1-2HB1The DISTANCE action with label S1-2HB1 calculates the following quantities:
 Quantity   
 Type   
 Description  
S1-2HB1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,6
S1-2HB2The DISTANCE action with label S1-2HB2 calculates the following quantities:
 Quantity   
 Type   
 Description  
S1-2HB2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,8
S1-2HB3The DISTANCE action with label S1-2HB3 calculates the following quantities:
 Quantity   
 Type   
 Description  
S1-2HB3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,9
S1-3HB1The DISTANCE action with label S1-3HB1 calculates the following quantities:
 Quantity   
 Type   
 Description  
S1-3HB1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,11
S1-3HB2The DISTANCE action with label S1-3HB2 calculates the following quantities:
 Quantity   
 Type   
 Description  
S1-3HB2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,13
S1-3HB3The DISTANCE action with label S1-3HB3 calculates the following quantities:
 Quantity   
 Type   
 Description  
S1-3HB3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,14

S2-1HB1The DISTANCE action with label S2-1HB1 calculates the following quantities:
 Quantity   
 Type   
 Description  
S2-1HB1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,1
S2-1HB2The DISTANCE action with label S2-1HB2 calculates the following quantities:
 Quantity   
 Type   
 Description  
S2-1HB2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,3
S2-1HB3The DISTANCE action with label S2-1HB3 calculates the following quantities:
 Quantity   
 Type   
 Description  
S2-1HB3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,4
S2-3HB1The DISTANCE action with label S2-3HB1 calculates the following quantities:
 Quantity   
 Type   
 Description  
S2-3HB1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,11
S2-3HB2The DISTANCE action with label S2-3HB2 calculates the following quantities:
 Quantity   
 Type   
 Description  
S2-3HB2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,13
S2-3HB3The DISTANCE action with label S2-3HB3 calculates the following quantities:
 Quantity   
 Type   
 Description  
S2-3HB3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,14

S3-2HB1The DISTANCE action with label S3-2HB1 calculates the following quantities:
 Quantity   
 Type   
 Description  
S3-2HB1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,6
S3-2HB2The DISTANCE action with label S3-2HB2 calculates the following quantities:
 Quantity   
 Type   
 Description  
S3-2HB2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,8
S3-2HB3The DISTANCE action with label S3-2HB3 calculates the following quantities:
 Quantity   
 Type   
 Description  
S3-2HB3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,9
S3-1HB1The DISTANCE action with label S3-1HB1 calculates the following quantities:
 Quantity   
 Type   
 Description  
S3-1HB1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,1
S3-1HB2The DISTANCE action with label S3-1HB2 calculates the following quantities:
 Quantity   
 Type   
 Description  
S3-1HB2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,3
S3-1HB3The DISTANCE action with label S3-1HB3 calculates the following quantities:
 Quantity   
 Type   
 Description  
S3-1HB3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,4

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
=S1-2HB1,S1-2HB2,S1-2HB3,S1-3HB1,S1-3HB2,S1-3HB3,S2-1HB1,S2-1HB2,S2-1HB3,S2-3HB1,S2-3HB2,S2-3HB3,S3-2HB1,S3-2HB2,S3-2HB3,S3-1HB1,S3-1HB2,S3-1HB3
    
AT
the positions of the wall
=0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3
    
KAPPA
the force constant for the wall
=50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall_S-HBThe LOWER_WALLS action with label lwall_S-HB calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall_S-HB.bias
scalar
the instantaneous value of the bias potential
lwall_S-HB.force2
scalar
the instantaneous value of the squared force due to this bias potential
... LOWER_WALLS

####################
### Lower Walls  ###
###   S - HB     ###
####################

S1-CB2The DISTANCE action with label S1-CB2 calculates the following quantities:
 Quantity   
 Type   
 Description  
S1-CB2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,7
S1-CB3The DISTANCE action with label S1-CB3 calculates the following quantities:
 Quantity   
 Type   
 Description  
S1-CB3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,12

S2-CB1The DISTANCE action with label S2-CB1 calculates the following quantities:
 Quantity   
 Type   
 Description  
S2-CB1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,2
S2-CB3The DISTANCE action with label S2-CB3 calculates the following quantities:
 Quantity   
 Type   
 Description  
S2-CB3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,12

S3-CB1The DISTANCE action with label S3-CB1 calculates the following quantities:
 Quantity   
 Type   
 Description  
S3-CB1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,2
S3-CB2The DISTANCE action with label S3-CB2 calculates the following quantities:
 Quantity   
 Type   
 Description  
S3-CB2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,7

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
=S1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2
    
AT
the positions of the wall
=0.3,0.3,0.3,0.3,0.3,0.3
    
KAPPA
the force constant for the wall
=50000,50000,50000,50000,50000,50000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall_S-CBThe LOWER_WALLS action with label lwall_S-CB calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall_S-CB.bias
scalar
the instantaneous value of the bias potential
lwall_S-CB.force2
scalar
the instantaneous value of the squared force due to this bias potential
... LOWER_WALLS

### Print dist+coord and wall-bias ###
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=S1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2,lwall_S-CB.bias,lwall_S-HB.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=cb-s_hb-s_dist.dat

#####################
### S-Na distance ###
#####################

### CYS1-Na ### 
nd1The DISTANCE action with label nd1 calculates the following quantities:
 Quantity   
 Type   
 Description  
nd1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,2650
### CYS2-Na ### 
nd2The DISTANCE action with label nd2 calculates the following quantities:
 Quantity   
 Type   
 Description  
nd2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,2650
### CYS3-Na ###
nd3The DISTANCE action with label nd3 calculates the following quantities:
 Quantity   
 Type   
 Description  
nd3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,2650

# Upper Walls distances
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
=nd1,nd2,nd3 
	
AT
the positions of the wall
=1.2,1.2,1.2 
	
KAPPA
the force constant for the wall
=100000.0,100000.0,100000.0
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall-ndistThe LOWER_WALLS action with label lwall-ndist calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall-ndist.bias
scalar
the instantaneous value of the bias potential
lwall-ndist.force2
scalar
the instantaneous value of the squared force due to this bias potential
... LOWER_WALLS

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=nd1,nd2,nd3,lwall-ndist.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=ndist.dat

####################
### Metadynamics ###
####################
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3
 
HEIGHT
the heights of the Gaussian hills
=0.5
 
SIGMA
the widths of the Gaussian hills
=0.02,0.02,0.02
 
GRID_MIN
the lower bounds for the grid
=0.15,0.15,0.15
 
GRID_MAX
the upper bounds for the grid
=0.7,0.7,0.7
 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.005,0.005,0.005
 
PACE
the frequency for hill addition
=250
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
 
WALKERS_N
number of walkers
=24
 
WALKERS_ID
walker id
=0
 
WALKERS_DIR
shared directory with the hills files from all the walkers
 
WALKERS_RSTRIDE
stride for reading hills files
=500
... METAD
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3
 
HEIGHT
the heights of the Gaussian hills
=0.5
 
SIGMA
the widths of the Gaussian hills
=0.02,0.02,0.02
 
GRID_MIN
the lower bounds for the grid
=0.15,0.15,0.15
 
GRID_MAX
the upper bounds for the grid
=0.7,0.7,0.7
 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.005,0.005,0.005
 
PACE
the frequency for hill addition
=250
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
 
WALKERS_N
number of walkers
=24
 
WALKERS_ID
walker id
=0
 
WALKERS_DIR
shared directory with the hills files from all the walkers
 
WALKERS_RSTRIDE
stride for reading hills files
=500
 
FILE
 a file in which the list of added hills is stored
=HILLS
... METAD

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,metad.bias,cys1-coord.mean,cys2-coord.mean,cys3-coord.mean,lwall-HB.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=colvar