PLUMED-NEST

Project ID: plumID:21.011
Source: NaCl_at_graphite-cmumd/coordination-profiles.plmd
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

# Define atom groups
graThe GROUP action with label gra calculates the following quantities:
 Quantity   
 Type   
 Description  
gra
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
=1-9152:1 
watThe GROUP action with label wat calculates the following quantities:
 Quantity   
 Type   
 Description  
wat
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
=9153-43319:3
sodThe GROUP action with label sod calculates the following quantities:
 Quantity   
 Type   
 Description  
sod
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
=43320-43737:1
chlThe GROUP action with label chl calculates the following quantities:
 Quantity   
 Type   
 Description  
chl
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
=43738-44155:1
sltThe GROUP action with label slt calculates the following quantities:
 Quantity   
 Type   
 Description  
slt
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
=43320-44155:1
slnThe GROUP action with label sln calculates the following quantities:
 Quantity   
 Type   
 Description  
sln
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
=9153-44155:1 

# Set a virtual atom at the origin and in the 'bulk'
p0The FIXEDATOM action with label p0 calculates the following quantities:
 Quantity   
 Type   
 Description  
p0
atoms
virtual atom calculated by FIXEDATOM action: 
FIXEDATOM
Add a virtual atom in a fixed position. This action has hidden defaults. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,7.403535
p0: 
FIXEDATOM
Add a virtual atom in a fixed position. This action uses the defaults shown here. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,7.403535  
SET_MASS
 mass of the virtual atom
=1 
SET_CHARGE
 charge of the virtual atom
=0
p1The FIXEDATOM action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1
atoms
virtual atom calculated by FIXEDATOM action: 
FIXEDATOM
Add a virtual atom in a fixed position. This action has hidden defaults. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,11.403535
p1: 
FIXEDATOM
Add a virtual atom in a fixed position. This action uses the defaults shown here. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,11.403535  
SET_MASS
 mass of the virtual atom
=1 
SET_CHARGE
 charge of the virtual atom
=0

# Get the coordination number distributions
cn0The COORDINATIONNUMBER action with label cn0 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn0
vector
the value calculated by this action:  
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=sod 
SPECIESB
this keyword is used for colvars such as the coordination number
=chl 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.355 NN=32 MM=64}
# PLUMED interprets the command:
# cn0:  COORDINATIONNUMBER SPECIESA=sod SPECIESB=chl SWITCH={RATIONAL R_0=0.355 NN=32 MM=64}
# as follows (Click the red comment above to revert to the short version of the input):
cn0_grpThe GROUP action with label cn0_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cn0_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
=sod 
cn0_matThe CONTACT_MATRIX action with label cn0_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cn0_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
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.355 NN=32 MM=64} 
cn0_onesThe CONSTANT action with label cn0_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cn0_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
=418
cn0The MATRIX_VECTOR_PRODUCT action with label cn0 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn0
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
=cn0_mat,cn0_ones 
cn0_caverageThe MEAN action with label cn0_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cn0_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
=cn0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- cn1The COORDINATIONNUMBER action with label cn1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1
vector
the value calculated by this action:  
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=sod 
SPECIESB
this keyword is used for colvars such as the coordination number
=wat 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.325 NN=32 MM=64}
# PLUMED interprets the command:
# cn1:  COORDINATIONNUMBER SPECIESA=sod SPECIESB=wat SWITCH={RATIONAL R_0=0.325 NN=32 MM=64}
# as follows (Click the red comment above to revert to the short version of the input):
cn1_grpThe GROUP action with label cn1_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1_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
=sod 
cn1_matThe CONTACT_MATRIX action with label cn1_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1_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
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.325 NN=32 MM=64} 
cn1_onesThe CONSTANT action with label cn1_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1_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
=11389
cn1The MATRIX_VECTOR_PRODUCT action with label cn1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1
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
=cn1_mat,cn1_ones 
cn1_caverageThe MEAN action with label cn1_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1_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
=cn1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- cn2The COORDINATIONNUMBER action with label cn2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn2
vector
the value calculated by this action:  
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=chl 
SPECIESB
this keyword is used for colvars such as the coordination number
=wat 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.385 NN=32 MM=64}
# PLUMED interprets the command:
# cn2:  COORDINATIONNUMBER SPECIESA=chl SPECIESB=wat SWITCH={RATIONAL R_0=0.385 NN=32 MM=64}
# as follows (Click the red comment above to revert to the short version of the input):
cn2_grpThe GROUP action with label cn2_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cn2_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
=chl 
cn2_matThe CONTACT_MATRIX action with label cn2_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cn2_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
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.385 NN=32 MM=64} 
cn2_onesThe CONSTANT action with label cn2_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cn2_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
=11389
cn2The MATRIX_VECTOR_PRODUCT action with label cn2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn2
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
=cn2_mat,cn2_ones 
cn2_caverageThe MEAN action with label cn2_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cn2_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
=cn2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- cn3The COORDINATIONNUMBER action with label cn3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn3
vector
the value calculated by this action:  
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=sod 
SPECIESB
this keyword is used for colvars such as the coordination number
=gra 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.365 NN=32 MM=64}
# PLUMED interprets the command:
# cn3:  COORDINATIONNUMBER SPECIESA=sod SPECIESB=gra SWITCH={RATIONAL R_0=0.365 NN=32 MM=64}
# as follows (Click the red comment above to revert to the short version of the input):
cn3_grpThe GROUP action with label cn3_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cn3_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
=sod 
cn3_matThe CONTACT_MATRIX action with label cn3_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cn3_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
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.365 NN=32 MM=64} 
cn3_onesThe CONSTANT action with label cn3_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cn3_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
=9152
cn3The MATRIX_VECTOR_PRODUCT action with label cn3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn3
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
=cn3_mat,cn3_ones 
cn3_caverageThe MEAN action with label cn3_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cn3_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
=cn3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- ipsThe MFILTER_MORE action with label ips calculates the following quantities:
 Quantity   
 Type   
 Description  
ips
vector
the value calculated by this action: 
MFILTER_MORE
Basically equivalent to MORE_THAN. This action is a shortcut. More details
 
DATA
the vector you wish to transform
=cn0 
SWITCH
the switching function that transform
={GAUSSIAN D_0=0.9999 R_0=0.00001}
# PLUMED interprets the command:
# ips: MFILTER_MORE DATA=cn0 SWITCH={GAUSSIAN D_0=0.9999 R_0=0.00001}
# as follows (Click the red comment above to revert to the short version of the input):
ips_grpThe GROUP action with label ips_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
ips_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
=cn0_grp 
ipsThe MORE_THAN action with label ips calculates the following quantities:
 Quantity   
 Type   
 Description  
ips
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the input to this function
=cn0 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={GAUSSIAN D_0=0.9999 R_0=0.00001} 
# --- End of included input --- 
densnaclThe MULTICOLVARDENS action with label densnacl calculates the following quantities:
 Quantity   
 Type   
 Description  
densnacl
grid
the average value of the order parameters at each point on the grid: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and it has hidden defaults. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn0 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densnacl: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and uses the defaults shown here. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn0 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1  
CLEAR
 the frequency with which to clear the density
=0
# PLUMED interprets the command:
# densnacl: MULTICOLVARDENS DATA=cn0 ORIGIN=p0 DIR=z NBINS=1480 KERNEL=GAUSSIAN BANDWIDTH=0.03 NORMALIZATION=true STRIDE=1
# as follows (Click the red comment above to revert to the short version of the input):
densnacl_distThe DISTANCE action with label densnacl_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
densnacl_dist.x
vector
the x-component of the vector connecting the two atoms
densnacl_dist.y
vector
the y-component of the vector connecting the two atoms
densnacl_dist.z
vector
the z-component of the vector connecting the two atoms: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
ORIGIN
calculate the distance of all the atoms specified using the ATOMS keyword from this point
=p0 
ATOMS
the pairs of atoms that you would like to calculate the angles for
=cn0 
densnacl_inumerThe KDE action with label densnacl_inumer calculates the following quantities:
 Quantity   
 Type   
 Description  
densnacl_inumer
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
VOLUMES
this keyword take the label of an action that calculates a vector of values
=cn0 
ARG
the input for this action is the scalar output from one or more other actions
=densnacl_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
densnacl_numerThe ACCUMULATE action with label densnacl_numer calculates the following quantities:
 Quantity   
 Type   
 Description  
densnacl_numer
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densnacl_inumer 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densnacl_kdeThe KDE action with label densnacl_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
densnacl_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
ARG
the input for this action is the scalar output from one or more other actions
=densnacl_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
densnacl_denomThe ACCUMULATE action with label densnacl_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
densnacl_denom
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densnacl_kde 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densnaclThe CUSTOM action with label densnacl calculates the following quantities:
 Quantity   
 Type   
 Description  
densnacl
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=densnacl_numer,densnacl_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- densnaowThe MULTICOLVARDENS action with label densnaow calculates the following quantities:
 Quantity   
 Type   
 Description  
densnaow
grid
the average value of the order parameters at each point on the grid: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and it has hidden defaults. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn1 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densnaow: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and uses the defaults shown here. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn1 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1  
CLEAR
 the frequency with which to clear the density
=0
# PLUMED interprets the command:
# densnaow: MULTICOLVARDENS DATA=cn1 ORIGIN=p0 DIR=z NBINS=1480 KERNEL=GAUSSIAN BANDWIDTH=0.03 NORMALIZATION=true STRIDE=1
# as follows (Click the red comment above to revert to the short version of the input):
densnaow_distThe DISTANCE action with label densnaow_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
densnaow_dist.x
vector
the x-component of the vector connecting the two atoms
densnaow_dist.y
vector
the y-component of the vector connecting the two atoms
densnaow_dist.z
vector
the z-component of the vector connecting the two atoms: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
ORIGIN
calculate the distance of all the atoms specified using the ATOMS keyword from this point
=p0 
ATOMS
the pairs of atoms that you would like to calculate the angles for
=cn1 
densnaow_inumerThe KDE action with label densnaow_inumer calculates the following quantities:
 Quantity   
 Type   
 Description  
densnaow_inumer
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
VOLUMES
this keyword take the label of an action that calculates a vector of values
=cn1 
ARG
the input for this action is the scalar output from one or more other actions
=densnaow_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
densnaow_numerThe ACCUMULATE action with label densnaow_numer calculates the following quantities:
 Quantity   
 Type   
 Description  
densnaow_numer
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densnaow_inumer 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densnaow_kdeThe KDE action with label densnaow_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
densnaow_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
ARG
the input for this action is the scalar output from one or more other actions
=densnaow_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
densnaow_denomThe ACCUMULATE action with label densnaow_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
densnaow_denom
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densnaow_kde 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densnaowThe CUSTOM action with label densnaow calculates the following quantities:
 Quantity   
 Type   
 Description  
densnaow
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=densnaow_numer,densnaow_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- densclowThe MULTICOLVARDENS action with label densclow calculates the following quantities:
 Quantity   
 Type   
 Description  
densclow
grid
the average value of the order parameters at each point on the grid: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and it has hidden defaults. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn2 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densclow: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and uses the defaults shown here. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn2 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1  
CLEAR
 the frequency with which to clear the density
=0
# PLUMED interprets the command:
# densclow: MULTICOLVARDENS DATA=cn2 ORIGIN=p0 DIR=z NBINS=1480 KERNEL=GAUSSIAN BANDWIDTH=0.03 NORMALIZATION=true STRIDE=1
# as follows (Click the red comment above to revert to the short version of the input):
densclow_distThe DISTANCE action with label densclow_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
densclow_dist.x
vector
the x-component of the vector connecting the two atoms
densclow_dist.y
vector
the y-component of the vector connecting the two atoms
densclow_dist.z
vector
the z-component of the vector connecting the two atoms: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
ORIGIN
calculate the distance of all the atoms specified using the ATOMS keyword from this point
=p0 
ATOMS
the pairs of atoms that you would like to calculate the angles for
=cn2 
densclow_inumerThe KDE action with label densclow_inumer calculates the following quantities:
 Quantity   
 Type   
 Description  
densclow_inumer
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
VOLUMES
this keyword take the label of an action that calculates a vector of values
=cn2 
ARG
the input for this action is the scalar output from one or more other actions
=densclow_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
densclow_numerThe ACCUMULATE action with label densclow_numer calculates the following quantities:
 Quantity   
 Type   
 Description  
densclow_numer
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densclow_inumer 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densclow_kdeThe KDE action with label densclow_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
densclow_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
ARG
the input for this action is the scalar output from one or more other actions
=densclow_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
densclow_denomThe ACCUMULATE action with label densclow_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
densclow_denom
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densclow_kde 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densclowThe CUSTOM action with label densclow calculates the following quantities:
 Quantity   
 Type   
 Description  
densclow
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=densclow_numer,densclow_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- densnagraThe MULTICOLVARDENS action with label densnagra calculates the following quantities:
 Quantity   
 Type   
 Description  
densnagra
grid
the average value of the order parameters at each point on the grid: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and it has hidden defaults. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn3 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densnagra: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and uses the defaults shown here. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn3 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1  
CLEAR
 the frequency with which to clear the density
=0
# PLUMED interprets the command:
# densnagra: MULTICOLVARDENS DATA=cn3 ORIGIN=p0 DIR=z NBINS=1480 KERNEL=GAUSSIAN BANDWIDTH=0.03 NORMALIZATION=true STRIDE=1
# as follows (Click the red comment above to revert to the short version of the input):
densnagra_distThe DISTANCE action with label densnagra_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
densnagra_dist.x
vector
the x-component of the vector connecting the two atoms
densnagra_dist.y
vector
the y-component of the vector connecting the two atoms
densnagra_dist.z
vector
the z-component of the vector connecting the two atoms: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
ORIGIN
calculate the distance of all the atoms specified using the ATOMS keyword from this point
=p0 
ATOMS
the pairs of atoms that you would like to calculate the angles for
=cn3 
densnagra_inumerThe KDE action with label densnagra_inumer calculates the following quantities:
 Quantity   
 Type   
 Description  
densnagra_inumer
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
VOLUMES
this keyword take the label of an action that calculates a vector of values
=cn3 
ARG
the input for this action is the scalar output from one or more other actions
=densnagra_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
densnagra_numerThe ACCUMULATE action with label densnagra_numer calculates the following quantities:
 Quantity   
 Type   
 Description  
densnagra_numer
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densnagra_inumer 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densnagra_kdeThe KDE action with label densnagra_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
densnagra_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
ARG
the input for this action is the scalar output from one or more other actions
=densnagra_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
densnagra_denomThe ACCUMULATE action with label densnagra_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
densnagra_denom
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densnagra_kde 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densnagraThe CUSTOM action with label densnagra calculates the following quantities:
 Quantity   
 Type   
 Description  
densnagra
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=densnagra_numer,densnagra_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- densipsThe MULTICOLVARDENS action with label densips calculates the following quantities:
 Quantity   
 Type   
 Description  
densips
grid
the average value of the order parameters at each point on the grid: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and it has hidden defaults. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=ips 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densips: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. This action is a shortcut and uses the defaults shown here. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=ips 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1  
CLEAR
 the frequency with which to clear the density
=0
# PLUMED interprets the command:
# densips: MULTICOLVARDENS DATA=ips ORIGIN=p0 DIR=z NBINS=1480 KERNEL=GAUSSIAN BANDWIDTH=0.03 NORMALIZATION=true STRIDE=1
# as follows (Click the red comment above to revert to the short version of the input):
densips_distThe DISTANCE action with label densips_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
densips_dist.x
vector
the x-component of the vector connecting the two atoms
densips_dist.y
vector
the y-component of the vector connecting the two atoms
densips_dist.z
vector
the z-component of the vector connecting the two atoms: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
ORIGIN
calculate the distance of all the atoms specified using the ATOMS keyword from this point
=p0 
ATOMS
the pairs of atoms that you would like to calculate the angles for
=ips 
densips_inumerThe KDE action with label densips_inumer calculates the following quantities:
 Quantity   
 Type   
 Description  
densips_inumer
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
VOLUMES
this keyword take the label of an action that calculates a vector of values
=ips 
ARG
the input for this action is the scalar output from one or more other actions
=densips_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
densips_numerThe ACCUMULATE action with label densips_numer calculates the following quantities:
 Quantity   
 Type   
 Description  
densips_numer
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densips_inumer 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densips_kdeThe KDE action with label densips_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
densips_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
ARG
the input for this action is the scalar output from one or more other actions
=densips_dist.z 
GRID_BIN
the number of bins for the grid
=1480 
densips_denomThe ACCUMULATE action with label densips_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
densips_denom
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=densips_kde 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
densipsThe CUSTOM action with label densips calculates the following quantities:
 Quantity   
 Type   
 Description  
densips
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=densips_numer,densips_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densnacl 
FILE
 the file on which to write the grid
=DENSna-cl.dat
The DUMPGRID action with label  calculates something
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densnaow 
FILE
 the file on which to write the grid
=DENSna-ow.dat
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densclow 
FILE
 the file on which to write the grid
=DENScl-ow.dat
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densnagra 
FILE
 the file on which to write the grid
=DENSna-gra.dat
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densips 
FILE
 the file on which to write the grid
=DENSips.dat