PLUMED-NEST-TEST-SITE

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
gra: 
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 
The GROUP action with label gra calculates somethingwat: 
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
The GROUP action with label wat calculates somethingsod: 
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
The GROUP action with label sod calculates somethingchl: 
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
The GROUP action with label chl calculates somethingslt: 
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
The GROUP action with label slt calculates somethingsln: 
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'
The GROUP action with label sln calculates somethingp0: 
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
The FIXEDATOM action with label p0 calculates somethingp0: 
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
p1: 
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
The FIXEDATOM action with label p1 calculates somethingp1: 
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
cn0:  
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):
The COORDINATIONNUMBER action with label cn0 calculates the following quantities:
 Quantity   
 Description  cn0_grp: 
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 
The GROUP action with label cn0_grp calculates somethingcn0_mat: 
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} 
The CONTACT_MATRIX action with label cn0_mat calculates the following quantities:
 Quantity   
 Description  
cn0_mat.value
a matrix containing the weights for the bonds between each pair of atomscn0_ones: 
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
The ONES action with label cn0_ones calculates the following quantities:
 Quantity   
 Description  
cn0_ones.value
a vector of ones with the required number of elementscn0: 
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_caverage: 
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 --- The MEAN action with label cn0_caverage calculates the following quantities:
 Quantity   
 Description  
cn0_caverage.value
the sumcn1:  
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):
The COORDINATIONNUMBER action with label cn1 calculates the following quantities:
 Quantity   
 Description  cn1_grp: 
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 
The GROUP action with label cn1_grp calculates somethingcn1_mat: 
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} 
The CONTACT_MATRIX action with label cn1_mat calculates the following quantities:
 Quantity   
 Description  
cn1_mat.value
a matrix containing the weights for the bonds between each pair of atomscn1_ones: 
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
The ONES action with label cn1_ones calculates the following quantities:
 Quantity   
 Description  
cn1_ones.value
a vector of ones with the required number of elementscn1: 
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_caverage: 
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 --- The MEAN action with label cn1_caverage calculates the following quantities:
 Quantity   
 Description  
cn1_caverage.value
the sumcn2:  
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):
The COORDINATIONNUMBER action with label cn2 calculates the following quantities:
 Quantity   
 Description  cn2_grp: 
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 
The GROUP action with label cn2_grp calculates somethingcn2_mat: 
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} 
The CONTACT_MATRIX action with label cn2_mat calculates the following quantities:
 Quantity   
 Description  
cn2_mat.value
a matrix containing the weights for the bonds between each pair of atomscn2_ones: 
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
The ONES action with label cn2_ones calculates the following quantities:
 Quantity   
 Description  
cn2_ones.value
a vector of ones with the required number of elementscn2: 
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_caverage: 
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 --- The MEAN action with label cn2_caverage calculates the following quantities:
 Quantity   
 Description  
cn2_caverage.value
the sumcn3:  
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):
The COORDINATIONNUMBER action with label cn3 calculates the following quantities:
 Quantity   
 Description  cn3_grp: 
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 
The GROUP action with label cn3_grp calculates somethingcn3_mat: 
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} 
The CONTACT_MATRIX action with label cn3_mat calculates the following quantities:
 Quantity   
 Description  
cn3_mat.value
a matrix containing the weights for the bonds between each pair of atomscn3_ones: 
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
The ONES action with label cn3_ones calculates the following quantities:
 Quantity   
 Description  
cn3_ones.value
a vector of ones with the required number of elementscn3: 
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_caverage: 
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 --- The MEAN action with label cn3_caverage calculates the following quantities:
 Quantity   
 Description  
cn3_caverage.value
the sumips: 
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):
The MFILTER_MORE action with label ips calculates the following quantities:
 Quantity   
 Description  ips_grp: 
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 
The GROUP action with label ips_grp calculates somethingips: 
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 --- 
densnacl: 
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
The MULTICOLVARDENS action with label densnacl calculates the following quantities:
 Quantity   
 Description  
densnacl.value
the average value of the order parameters at each point on the griddensnacl: 
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_dist: 
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 
The DISTANCES action with label densnacl_dist calculates the following quantities:
 Quantity   
 Description  
densnacl_dist.x
the x-components of the distance vectors
densnacl_dist.y
the y-components of the distance vectors
densnacl_dist.z
the z-components of the distance vectorsdensnacl_inumer: 
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 
The KDE action with label densnacl_inumer calculates the following quantities:
 Quantity   
 Description  
densnacl_inumer.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensnacl_numer: 
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 
The ACCUMULATE action with label densnacl_numer calculates the following quantities:
 Quantity   
 Description  
densnacl_numer.value
a sum calculated from the time series of the input quantitydensnacl_kde: 
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 
The KDE action with label densnacl_kde calculates the following quantities:
 Quantity   
 Description  
densnacl_kde.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensnacl_denom: 
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 
The ACCUMULATE action with label densnacl_denom calculates the following quantities:
 Quantity   
 Description  
densnacl_denom.value
a sum calculated from the time series of the input quantitydensnacl: 
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 --- densnaow: 
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
The MULTICOLVARDENS action with label densnaow calculates the following quantities:
 Quantity   
 Description  
densnaow.value
the average value of the order parameters at each point on the griddensnaow: 
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_dist: 
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 
The DISTANCES action with label densnaow_dist calculates the following quantities:
 Quantity   
 Description  
densnaow_dist.x
the x-components of the distance vectors
densnaow_dist.y
the y-components of the distance vectors
densnaow_dist.z
the z-components of the distance vectorsdensnaow_inumer: 
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 
The KDE action with label densnaow_inumer calculates the following quantities:
 Quantity   
 Description  
densnaow_inumer.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensnaow_numer: 
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 
The ACCUMULATE action with label densnaow_numer calculates the following quantities:
 Quantity   
 Description  
densnaow_numer.value
a sum calculated from the time series of the input quantitydensnaow_kde: 
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 
The KDE action with label densnaow_kde calculates the following quantities:
 Quantity   
 Description  
densnaow_kde.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensnaow_denom: 
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 
The ACCUMULATE action with label densnaow_denom calculates the following quantities:
 Quantity   
 Description  
densnaow_denom.value
a sum calculated from the time series of the input quantitydensnaow: 
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 --- densclow: 
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
The MULTICOLVARDENS action with label densclow calculates the following quantities:
 Quantity   
 Description  
densclow.value
the average value of the order parameters at each point on the griddensclow: 
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_dist: 
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 
The DISTANCES action with label densclow_dist calculates the following quantities:
 Quantity   
 Description  
densclow_dist.x
the x-components of the distance vectors
densclow_dist.y
the y-components of the distance vectors
densclow_dist.z
the z-components of the distance vectorsdensclow_inumer: 
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 
The KDE action with label densclow_inumer calculates the following quantities:
 Quantity   
 Description  
densclow_inumer.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensclow_numer: 
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 
The ACCUMULATE action with label densclow_numer calculates the following quantities:
 Quantity   
 Description  
densclow_numer.value
a sum calculated from the time series of the input quantitydensclow_kde: 
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 
The KDE action with label densclow_kde calculates the following quantities:
 Quantity   
 Description  
densclow_kde.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensclow_denom: 
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 
The ACCUMULATE action with label densclow_denom calculates the following quantities:
 Quantity   
 Description  
densclow_denom.value
a sum calculated from the time series of the input quantitydensclow: 
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 --- densnagra: 
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
The MULTICOLVARDENS action with label densnagra calculates the following quantities:
 Quantity   
 Description  
densnagra.value
the average value of the order parameters at each point on the griddensnagra: 
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_dist: 
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 
The DISTANCES action with label densnagra_dist calculates the following quantities:
 Quantity   
 Description  
densnagra_dist.x
the x-components of the distance vectors
densnagra_dist.y
the y-components of the distance vectors
densnagra_dist.z
the z-components of the distance vectorsdensnagra_inumer: 
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 
The KDE action with label densnagra_inumer calculates the following quantities:
 Quantity   
 Description  
densnagra_inumer.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensnagra_numer: 
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 
The ACCUMULATE action with label densnagra_numer calculates the following quantities:
 Quantity   
 Description  
densnagra_numer.value
a sum calculated from the time series of the input quantitydensnagra_kde: 
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 
The KDE action with label densnagra_kde calculates the following quantities:
 Quantity   
 Description  
densnagra_kde.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensnagra_denom: 
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 
The ACCUMULATE action with label densnagra_denom calculates the following quantities:
 Quantity   
 Description  
densnagra_denom.value
a sum calculated from the time series of the input quantitydensnagra: 
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 --- densips: 
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
The MULTICOLVARDENS action with label densips calculates the following quantities:
 Quantity   
 Description  
densips.value
the average value of the order parameters at each point on the griddensips: 
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_dist: 
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 
The DISTANCES action with label densips_dist calculates the following quantities:
 Quantity   
 Description  
densips_dist.x
the x-components of the distance vectors
densips_dist.y
the y-components of the distance vectors
densips_dist.z
the z-components of the distance vectorsdensips_inumer: 
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 
The KDE action with label densips_inumer calculates the following quantities:
 Quantity   
 Description  
densips_inumer.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensips_numer: 
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 
The ACCUMULATE action with label densips_numer calculates the following quantities:
 Quantity   
 Description  
densips_numer.value
a sum calculated from the time series of the input quantitydensips_kde: 
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 
The KDE action with label densips_kde calculates the following quantities:
 Quantity   
 Description  
densips_kde.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsdensips_denom: 
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 
The ACCUMULATE action with label densips_denom calculates the following quantities:
 Quantity   
 Description  
densips_denom.value
a sum calculated from the time series of the input quantitydensips: 
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