PLUMED-NEST-TEST-SITE

Project ID: plumID:22.021
Source: IceVI-Liquid/5-BiasedCoexistence/COEX_10000.0atm/290.0K/plumed.strict.dat
Originally used with PLUMED version: 2.8
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

# Strict counting of molecules
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and it has hidden defaults. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-3840:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0575
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv2
 
REFERENCE_1
PDB files with relative distances from central atom
=env1.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4.pdb
 
REFERENCE_5
PDB files with relative distances from central atom
=env5.pdb
 
REFERENCE_6
PDB files with relative distances from central atom
=env6.pdb
 
REFERENCE_7
PDB files with relative distances from central atom
=env7.pdb
 
REFERENCE_8
PDB files with relative distances from central atom
=env8.pdb
 
REFERENCE_9
PDB files with relative distances from central atom
=env9.pdb
 
REFERENCE_10
PDB files with relative distances from central atom
=env10.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.730000 D_MAX=0.730001}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
The ENVIRONMENTSIMILARITY action with label refcv2 calculates the following quantities:
 Quantity   
 Description  
refcv2.morethan
the number of colvars that have a value more than a threshold
refcv2.mean
the mean of the colvars
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and uses the defaults shown here. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-3840:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0575
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv2
 
REFERENCE_1
PDB files with relative distances from central atom
=env1.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4.pdb
 
REFERENCE_5
PDB files with relative distances from central atom
=env5.pdb
 
REFERENCE_6
PDB files with relative distances from central atom
=env6.pdb
 
REFERENCE_7
PDB files with relative distances from central atom
=env7.pdb
 
REFERENCE_8
PDB files with relative distances from central atom
=env8.pdb
 
REFERENCE_9
PDB files with relative distances from central atom
=env9.pdb
 
REFERENCE_10
PDB files with relative distances from central atom
=env10.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.730000 D_MAX=0.730001}
 
MEAN
 calculate the mean of all the quantities
 
CUTOFF
 how many multiples of sigma would you like to consider beyond the maximum distance in the environment
=3 
LCUTOFF
 any atoms separated by less than this tolerance should be ignored
=0.0001 
LAMBDA
 Lambda parameter
=100
... ENVIRONMENTSIMILARITY
# PLUMED interprets the command:
# ENVIRONMENTSIMILARITY ...
#  SPECIES=1-3840:3
#  SIGMA=0.0575
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv2
#  REFERENCE_1=env1.pdb
#  REFERENCE_2=env2.pdb
#  REFERENCE_3=env3.pdb
#  REFERENCE_4=env4.pdb
#  REFERENCE_5=env5.pdb
#  REFERENCE_6=env6.pdb
#  REFERENCE_7=env7.pdb
#  REFERENCE_8=env8.pdb
#  REFERENCE_9=env9.pdb
#  REFERENCE_10=env10.pdb
#  MORE_THAN={CUBIC D_0=0.730000 D_MAX=0.730001}
#  MEAN
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
refcv2_cmat: 
DISTANCE_MATRIX
Calculate a matrix of distances More details
 
COMPONENTS
 also calculate the components of the vector connecting the atoms in the contact matrix
 
GROUP
the atoms for which you would like to calculate the adjacency matrix
=1-3840:3 
CUTOFF
 ignore distances that have a value larger than this cutoff
=0.456545 
The DISTANCE_MATRIX action with label refcv2_cmat calculates the following quantities:
 Quantity   
 Description  
refcv2_cmat.w
a matrix containing the weights for the bonds between each pair of atoms
refcv2_cmat.x
the projection of the bond on the x axis
refcv2_cmat.y
the projection of the bond on the y axis
refcv2_cmat.z
the projection of the bond on the z axis
refcv2_cmat.value
a matrix containing the weights for the bonds between each pair of atomsrefcv2_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
=1-3840:3 
The GROUP action with label refcv2_grp calculates somethingrefcv2_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
=1280
The ONES action with label refcv2_ones calculates the following quantities:
 Quantity   
 Description  
refcv2_ones.value
a vector of ones with the required number of elementsrefcv2_matenv1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x--0.174)^2+(y--0.007)^2+(z--0.221)^2)/(4*0.00330625))+exp(-((x-0.002)^2+(y-0.174)^2+(z-0.22)^2)/(4*0.00330625))+exp(-((x-0.175)^2+(y--0.009)^2+(z--0.216)^2)/(4*0.00330625))+exp(-((x-0.005)^2+(y--0.1814)^2+(z-0.214)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv1 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv1.value
an arbitrary functionrefcv2_env1: 
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
=refcv2_matenv1,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env1 calculates the following quantities:
 Quantity   
 Description  
refcv2_env1.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env1..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x--0.27)^2+(y-0.007)^2+(z-0.005)^2)/(4*0.00330625))+exp(-((x-0.179)^2+(y-0.173)^2+(z--0.125)^2)/(4*0.00330625))+exp(-((x-0.174)^2+(y-0.007)^2+(z-0.221)^2)/(4*0.00330625))+exp(-((x-0.179)^2+(y--0.1744)^2+(z--0.135)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv2 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv2.value
an arbitrary functionrefcv2_env2: 
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
=refcv2_matenv2,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env2 calculates the following quantities:
 Quantity   
 Description  
refcv2_env2.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env2..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x--0.27)^2+(y-0.008)^2+(z--0.005)^2)/(4*0.00330625))+exp(-((x-0.173)^2+(y-0.008)^2+(z--0.22)^2)/(4*0.00330625))+exp(-((x-0.182)^2+(y--0.167)^2+(z-0.135)^2)/(4*0.00330625))+exp(-((x-0.175)^2+(y-0.181)^2+(z-0.13)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv3 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv3.value
an arbitrary functionrefcv2_env3: 
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
=refcv2_matenv3,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env3 calculates the following quantities:
 Quantity   
 Description  
refcv2_env3.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env3..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv4: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x--0.175)^2+(y--0.009)^2+(z--0.215)^2)/(4*0.00330625))+exp(-((x--0.17)^2+(y--0.175)^2+(z-0.13)^2)/(4*0.00330625))+exp(-((x--0.17)^2+(y-0.173)^2+(z-0.14)^2)/(4*0.00330625))+exp(-((x-0.27)^2+(y--0.008)^2+(z-0.005)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv4 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv4.value
an arbitrary functionrefcv2_env4: 
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
=refcv2_matenv4,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env4 calculates the following quantities:
 Quantity   
 Description  
refcv2_env4.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env4..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv5: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x-0.002)^2+(y--0.27)^2+(z-0.005)^2)/(4*0.00330625))+exp(-((x-0.004)^2+(y-0.166)^2+(z-0.224)^2)/(4*0.00330625))+exp(-((x-0.17)^2+(y-0.175)^2+(z--0.13)^2)/(4*0.00330625))+exp(-((x--0.1784)^2+(y-0.173)^2+(z--0.125)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv5 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv5.value
an arbitrary functionrefcv2_env5: 
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
=refcv2_matenv5,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env5 calculates the following quantities:
 Quantity   
 Description  
refcv2_env5.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env5..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv6: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x-0.27)^2+(y--0.007)^2+(z--0.005)^2)/(4*0.00330625))+exp(-((x--0.1734)^2+(y-0)^2+(z-0.216)^2)/(4*0.00330625))+exp(-((x--0.1734)^2+(y-0.166)^2+(z--0.139)^2)/(4*0.00330625))+exp(-((x--0.1644)^2+(y--0.1734)^2+(z--0.139)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv6 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv6.value
an arbitrary functionrefcv2_env6: 
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
=refcv2_matenv6,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env6 calculates the following quantities:
 Quantity   
 Description  
refcv2_env6.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env6..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv7: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x-0.003)^2+(y-0.27)^2+(z--0.004)^2)/(4*0.00330625))+exp(-((x-0.17)^2+(y--0.175)^2+(z-0.13)^2)/(4*0.00330625))+exp(-((x--0.179)^2+(y--0.173)^2+(z-0.125)^2)/(4*0.00330625))+exp(-((x-0.004)^2+(y--0.166)^2+(z--0.2242)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv7 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv7.value
an arbitrary functionrefcv2_env7: 
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
=refcv2_matenv7,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env7 calculates the following quantities:
 Quantity   
 Description  
refcv2_env7.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env7..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv8: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x-0.175)^2+(y-0.009)^2+(z-0.215)^2)/(4*0.00330625))+exp(-((x--0.1734)^2+(y-0.007)^2+(z-0.22)^2)/(4*0.00330625))+exp(-((x-0.002)^2+(y--0.175)^2+(z--0.2202)^2)/(4*0.00330625))+exp(-((x-0.009)^2+(y-0.174)^2+(z--0.2152)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv8 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv8.value
an arbitrary functionrefcv2_env8: 
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
=refcv2_matenv8,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env8 calculates the following quantities:
 Quantity   
 Description  
refcv2_env8.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env8..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv9: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x--0.173)^2+(y-0.173)^2+(z-0.134)^2)/(4*0.00330625))+exp(-((x-0.175)^2+(y-0.181)^2+(z-0.129)^2)/(4*0.00330625))+exp(-((x--0.003)^2+(y--0.27)^2+(z-0.004)^2)/(4*0.00330625))+exp(-((x-0.001)^2+(y-0.173)^2+(z--0.2202)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv9 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv9.value
an arbitrary functionrefcv2_env9: 
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
=refcv2_matenv9,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env9 calculates the following quantities:
 Quantity   
 Description  
refcv2_env9.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env9..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2_matenv10: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(step(w-0.0001)*step(0.456545-w)/4)*(exp(-((x--0.002)^2+(y-0.27)^2+(z--0.005)^2)/(4*0.00330625))+exp(-((x-0.176)^2+(y--0.1804)^2+(z--0.13)^2)/(4*0.00330625))+exp(-((x--0.1804)^2+(y--0.1754)^2+(z--0.13)^2)/(4*0.00330625))+exp(-((x--0.007)^2+(y--0.1734)^2+(z-0.219)^2)/(4*0.00330625 
The CUSTOM action with label refcv2_matenv10 calculates the following quantities:
 Quantity   
 Description  
refcv2_matenv10.value
an arbitrary functionrefcv2_env10: 
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
=refcv2_matenv10,refcv2_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv2_env10 calculates the following quantities:
 Quantity   
 Description  
refcv2_env10.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv2_env10..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv2_env1,refcv2_env2,refcv2_env3,refcv2_env4,refcv2_env5,refcv2_env6,refcv2_env7,refcv2_env8,refcv2_env9,refcv2_env10 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
VAR
the names to give each of the arguments in the function
=v1,v2,v3,v4,v5,v6,v7,v8,v9,v10 
FUNC
the function you wish to evaluate
=(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4)+exp(100*v5)+exp(100*v6)+exp(100*v7)+exp(100*v8)+exp(100*v9)+exp(100*v10 
refcv2_mt: 
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
=refcv2 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={CUBIC D_0=0.730000 D_MAX=0.730001} 
The MORE_THAN action with label refcv2_mt calculates the following quantities:
 Quantity   
 Description  
refcv2_mt.value
a function that is one if the if the input is more than a thresholdrefcv2_morethan: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=refcv2_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The SUM action with label refcv2_morethan calculates the following quantities:
 Quantity   
 Description  
refcv2_morethan.value
the sumrefcv2_mean: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=refcv2 
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 refcv2_mean calculates the following quantities:
 Quantity   
 Description  
refcv2_mean.value
the sum