PLUMED-NEST

Project ID: plumID:21.002
Source: Crystallization/IceIh/288molecules/350K/plumed.start.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

#SETTINGS NREPLICAS=2
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box: 
VOLUME
Calculate the volume of the simulation box. More details

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
=1-864:3
 
SIGMA
 the width to use for the gaussian kernels
=0.05
 
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
=refcvThe ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv
vector
the environmental similar parameter for each of the input atoms
refcv_morethan
scalar
the number of colvars that have a value more than a threshold
refcv_mean
scalar
the mean of the colvars
 
REFERENCE_1
PDB files with relative distances from central atom
=env1h.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2h.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3h.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4h.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=0.5 NN=6 MM=12}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
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
=1-864:3
 
SIGMA
 the width to use for the gaussian kernels
=0.05
 
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
=refcv
 
REFERENCE_1
PDB files with relative distances from central atom
=env1h.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2h.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3h.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4h.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=0.5 NN=6 MM=12}
 
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=1-864:3
#  SIGMA=0.05
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv
#  REFERENCE_1=env1h.pdb
#  REFERENCE_2=env2h.pdb
#  REFERENCE_3=env3h.pdb
#  REFERENCE_4=env4h.pdb
#  MORE_THAN={RATIONAL R_0=0.5 NN=6 MM=12}
#  MEAN
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
refcv_cmatThe DISTANCE_MATRIX action with label refcv_cmat calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_cmat.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
refcv_cmat.x
matrix
the projection of the bond on the x axis
refcv_cmat.y
matrix
the projection of the bond on the y axis
refcv_cmat.z
matrix
the projection of the bond on the z axis: 
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
=1-864:3 
CUTOFF
 ignore distances that have a value larger than this cutoff
=0.6085
refcv_grpThe GROUP action with label refcv_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_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
=1-864:3
refcv_onesThe CONSTANT action with label refcv_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_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
=288
refcv_matenv1The CUSTOM action with label refcv_matenv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv1
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_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(0.6085-w)/17)*(exp(-((x--0.4486)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.4585)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.0025
refcv_env1The MATRIX_VECTOR_PRODUCT action with label refcv_env1 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env1
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv1,refcv_ones
refcv_matenv2The CUSTOM action with label refcv_matenv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv2
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_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(0.6085-w)/17)*(exp(-((x--0.4486)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.4585)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.0025
refcv_env2The MATRIX_VECTOR_PRODUCT action with label refcv_env2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env2
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv2,refcv_ones
refcv_matenv3The CUSTOM action with label refcv_matenv3 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv3
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_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(0.6085-w)/17)*(exp(-((x--0.4485)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.4585)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.0025
refcv_env3The MATRIX_VECTOR_PRODUCT action with label refcv_env3 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env3
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv3,refcv_ones
refcv_matenv4The CUSTOM action with label refcv_matenv4 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv4
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_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(0.6085-w)/17)*(exp(-((x--0.4485)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.4585)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.0025
refcv_env4The MATRIX_VECTOR_PRODUCT action with label refcv_env4 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env4
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv4,refcv_ones
refcvThe CUSTOM action with label refcv calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=refcv_env1,refcv_env2,refcv_env3,refcv_env4 
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 
FUNC
the function you wish to evaluate
=(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4
refcv_mtThe MORE_THAN action with label refcv_mt calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_mt
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 values input to this function
=refcv 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=0.5 NN=6 MM=12}
refcv_morethanThe SUM action with label refcv_morethan calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_morethan
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values input to this function
=refcv_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
refcv_meanThe MEAN action with label refcv_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_mean
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the values input to this function
=refcv 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- End of included input --- 
# Construct a bias potential

energyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the internal energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details

# Construct a bias potential using VES
#
# Basis functions

bf1: 
BF_LEGENDRE
Legendre polynomials basis functions. More details
 
ORDER
The order of the basis function expansion
=40 
MINIMUM
The minimum of the interval on which the basis functions are defined
=0.0 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=288.0

# Target distribution

The BF_LEGENDRE action with label bf1 calculates somethingtd_uni: 
TD_UNIFORM
Uniform target distribution (static). More details

# Expansion

The TD_UNIFORM action with label td_uni calculates something
VES_LINEAR_EXPANSION
Linear basis set expansion bias. More details
 ...
 
ARG
the labels of the scalars on which the bias will act
=refcv.morethan
 
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bf1
 
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=350.0
 
GRID_BINS
the number of bins used for the grid
=300
 
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_uni
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1.bias
scalar
the instantaneous value of the bias potential
b1.force2
scalar
the instantaneous value of the squared force due to this bias potential.
... VES_LINEAR_EXPANSION

# Optimization algorithm

OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. This action has hidden defaults. More details
 ...
  
BIAS
the label of the VES bias to be optimized
=b1
  
STRIDE
the frequency of updating the coefficients given in the number of MD steps
=500
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=o1
  
STEPSIZE
the step size used for the optimization
=1
  
FES_OUTPUT
how often the FES(s) should be written out to file
=500
  
BIAS_OUTPUT
how often the bias(es) should be written out to file
=500
  
COEFFS_OUTPUT
 how often the coefficients should be written to file
=100
  #MULTIPLE_WALKERS
... OPT_AVERAGED_SGD
The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalar
OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. This action uses the defaults shown here. More details
 ...
  
BIAS
the label of the VES bias to be optimized
=b1
  
STRIDE
the frequency of updating the coefficients given in the number of MD steps
=500
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=o1
  
STEPSIZE
the step size used for the optimization
=1
  
FES_OUTPUT
how often the FES(s) should be written out to file
=500
  
BIAS_OUTPUT
how often the bias(es) should be written out to file
=500
  
COEFFS_OUTPUT
 how often the coefficients should be written to file
=100
  #MULTIPLE_WALKERS
 
COEFFS_FILE
 the name of output file for the coefficients
=coeffs.data
... OPT_AVERAGED_SGD

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
=1-864:3
 
SIGMA
 the width to use for the gaussian kernels
=0.05
 
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
=refcv2The ENVIRONMENTSIMILARITY action with label refcv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2
vector
the environmental similar parameter for each of the input atoms
refcv2_morethan
scalar
the number of colvars that have a value more than a threshold
refcv2_mean
scalar
the mean of the colvars
 
REFERENCE_1
PDB files with relative distances from central atom
=env1c.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2c.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=0.5 NN=6 MM=12}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
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
=1-864:3
 
SIGMA
 the width to use for the gaussian kernels
=0.05
 
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
=env1c.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2c.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=0.5 NN=6 MM=12}
 
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=1-864:3
#  SIGMA=0.05
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv2
#  REFERENCE_1=env1c.pdb
#  REFERENCE_2=env2c.pdb
#  MORE_THAN={RATIONAL R_0=0.5 NN=6 MM=12}
#  MEAN
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
refcv2_cmatThe DISTANCE_MATRIX action with label refcv2_cmat calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_cmat.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
refcv2_cmat.x
matrix
the projection of the bond on the x axis
refcv2_cmat.y
matrix
the projection of the bond on the y axis
refcv2_cmat.z
matrix
the projection of the bond on the z axis: 
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
=1-864:3 
CUTOFF
 ignore distances that have a value larger than this cutoff
=0.608694
refcv2_grpThe GROUP action with label refcv2_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_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
=1-864:3
refcv2_onesThe CONSTANT action with label refcv2_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_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
=288
refcv2_matenv1The CUSTOM action with label refcv2_matenv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv1
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values 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(0.608694-w)/16)*(exp(-((x--0.4585)^2+(y--0.0001)^2+(z-0.0019)^2)/(4*0.0025))+exp(-((x--0.2307)^2+(y--0.1316)^2+(z--0.3738)^2)/(4*0.0025))+exp(-((x--0.2296)^2+(y--0.1323)^2+(z--0.093)^2)/(4*0.0025))+exp(-((x--0.2293)^2+(y--0.3972)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2292)^2+(y-0.397)^2+(z-0.0018)^2)/(4*0.0025))+exp(-((x--0.2278)^2+(y-0.1314)^2+(z-0.3756)^2)/(4*0.0025))+exp(-((x--0.0015)^2+(y-0.2655)^2+(z--0.3737)^2)/(4*0.0025))+exp(-((x--0.0003)^2+(y-0.2649)^2+(z--0.093)^2)/(4*0.0025))+exp(-((x-0.0012)^2+(y--0.0008)^2+(z-0.2809)^2)/(4*0.0025))+exp(-((x-0.0015)^2+(y--0.2657)^2+(z-0.3739)^2)/(4*0.0025))+exp(-((x-0.2278)^2+(y--0.1316)^2+(z--0.3756)^2)/(4*0.0025))+exp(-((x-0.229)^2+(y--0.1323)^2+(z--0.0948)^2)/(4*0.0025))+exp(-((x-0.2293)^2+(y-0.397)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2294)^2+(y--0.3972)^2+(z--0.0018)^2)/(4*0.0025))+exp(-((x-0.2309)^2+(y-0.1314)^2+(z-0.3738)^2)/(4*0.0025))+exp(-((x-0.4586)^2+(y--0.0001)^2+(z--0.0018)^2)/(4*0.0025
refcv2_env1The MATRIX_VECTOR_PRODUCT action with label refcv2_env1 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env1
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv1,refcv2_ones
refcv2_matenv2The CUSTOM action with label refcv2_matenv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv2
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values 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(0.608694-w)/16)*(exp(-((x--0.4586)^2+(y-0.0001)^2+(z-0.0018)^2)/(4*0.0025))+exp(-((x--0.2308)^2+(y--0.1315)^2+(z--0.3739)^2)/(4*0.0025))+exp(-((x--0.2293)^2+(y--0.3971)^2+(z--0.0001)^2)/(4*0.0025))+exp(-((x--0.2293)^2+(y-0.3971)^2+(z-0.0018)^2)/(4*0.0025))+exp(-((x--0.229)^2+(y-0.1322)^2+(z-0.0947)^2)/(4*0.0025))+exp(-((x--0.2278)^2+(y-0.1315)^2+(z-0.3756)^2)/(4*0.0025))+exp(-((x--0.0015)^2+(y-0.2657)^2+(z--0.3739)^2)/(4*0.0025))+exp(-((x--0.0012)^2+(y-0.0008)^2+(z--0.2809)^2)/(4*0.0025))+exp(-((x-0.0003)^2+(y--0.2649)^2+(z-0.093)^2)/(4*0.0025))+exp(-((x-0.0015)^2+(y--0.2655)^2+(z-0.3737)^2)/(4*0.0025))+exp(-((x-0.2278)^2+(y--0.1315)^2+(z--0.3757)^2)/(4*0.0025))+exp(-((x-0.2292)^2+(y--0.3971)^2+(z--0.0019)^2)/(4*0.0025))+exp(-((x-0.2293)^2+(y-0.3971)^2+(z--0.0001)^2)/(4*0.0025))+exp(-((x-0.2297)^2+(y-0.1322)^2+(z-0.0929)^2)/(4*0.0025))+exp(-((x-0.2307)^2+(y-0.1315)^2+(z-0.3737)^2)/(4*0.0025))+exp(-((x-0.4585)^2+(y-0.0001)^2+(z--0.0019)^2)/(4*0.0025
refcv2_env2The MATRIX_VECTOR_PRODUCT action with label refcv2_env2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env2
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv2,refcv2_ones
refcv2The CUSTOM action with label refcv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=refcv2_env1,refcv2_env2 
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 
FUNC
the function you wish to evaluate
=(1/100)*log(exp(100*v1)+exp(100*v2
refcv2_mtThe MORE_THAN action with label refcv2_mt calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_mt
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 values input to this function
=refcv2 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=0.5 NN=6 MM=12}
refcv2_morethanThe SUM action with label refcv2_morethan calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_morethan
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values 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
refcv2_meanThe MEAN action with label refcv2_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_mean
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the values 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 --- 
diffThe MATHEVAL action with label diff calculates the following quantities:
 Quantity   
 Type   
 Description  
diff
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=refcv2.mean,refcv.mean 
FUNC
the function you wish to evaluate
=((x-0.2075)/(0.5821-0.2075)-(y-0.2319)/(0.8137-0.2319 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=diff 
AT
the positions of the wall
=0.05 
KAPPA
the force constant for the wall
=100000 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential

# Avoid other structures
Q6
Calculate sixth order Steinhardt parameters. This action is a shortcut. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-864:3 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=0.3 D_MAX=0.35} 
VMEAN
 calculate the norm of the mean vector
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=q6The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6
vector
the norms of the vectors of spherical harmonic coefficients
# PLUMED interprets the command:
# Q6 SPECIES=1-864:3 SWITCH={CUBIC D_0=0.3 D_MAX=0.35} VMEAN LABEL=q6
# as follows (Click the red comment above to revert to the short version of the input):
q6_grpThe GROUP action with label q6_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_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
=1-864:3
q6_matThe CONTACT_MATRIX action with label q6_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_mat.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
q6_mat.x
matrix
the projection of the bond on the x axis
q6_mat.y
matrix
the projection of the bond on the y axis
q6_mat.z
matrix
the projection of the bond on the z axis: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
GROUP
specifies the list of atoms that should be assumed indistinguishable
=1-864:3 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={CUBIC D_0=0.3 D_MAX=0.35} 
COMPONENTS
 also calculate the components of the vector connecting the atoms in the contact matrix
q6_shThe SPHERICAL_HARMONIC action with label q6_sh calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_sh.rm-n6
matrix
the real parts of the spherical harmonic values with the m value given  This is the n6th of these quantities
q6_sh.rm-n5
matrix
the real parts of the spherical harmonic values with the m value given  This is the n5th of these quantities
q6_sh.rm-n4
matrix
the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q6_sh.rm-n3
matrix
the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q6_sh.rm-n2
matrix
the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q6_sh.rm-n1
matrix
the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q6_sh.rm-0
matrix
the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q6_sh.rm-p1
matrix
the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q6_sh.rm-p2
matrix
the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q6_sh.rm-p3
matrix
the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q6_sh.rm-p4
matrix
the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q6_sh.rm-p5
matrix
the real parts of the spherical harmonic values with the m value given  This is the p5th of these quantities
q6_sh.rm-p6
matrix
the real parts of the spherical harmonic values with the m value given  This is the p6th of these quantities
q6_sh.im-n6
matrix
the real parts of the spherical harmonic values with the m value given  This is the n6th of these quantities
q6_sh.im-n5
matrix
the real parts of the spherical harmonic values with the m value given  This is the n5th of these quantities
q6_sh.im-n4
matrix
the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q6_sh.im-n3
matrix
the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q6_sh.im-n2
matrix
the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q6_sh.im-n1
matrix
the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q6_sh.im-0
matrix
the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q6_sh.im-p1
matrix
the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q6_sh.im-p2
matrix
the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q6_sh.im-p3
matrix
the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q6_sh.im-p4
matrix
the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q6_sh.im-p5
matrix
the real parts of the spherical harmonic values with the m value given  This is the p5th of these quantities
q6_sh.im-p6
matrix
the real parts of the spherical harmonic values with the m value given  This is the p6th of these quantities: 
SPHERICAL_HARMONIC
Calculate the values of all the spherical harmonic funtions for a particular value of l. More details
 
ARG
the values input to this function
=q6_mat.x,q6_mat.y,q6_mat.z,q6_mat.w 
L
the value of the angular momentum
=6
q6_denom_onesThe CONSTANT action with label q6_denom_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_denom_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
=288
q6_denomThe MATRIX_VECTOR_PRODUCT action with label q6_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_denom
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 label for the matrix and the vector/scalar that are being multiplied
=q6_mat.w,q6_denom_ones
q6_spThe MATRIX_VECTOR_PRODUCT action with label q6_sp calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_sp.rm-n6
vector
the product of the matrix q6_sh.rm-n6 and the vector q6_denom_ones
q6_sp.rm-n5
vector
the product of the matrix q6_sh.rm-n5 and the vector q6_denom_ones
q6_sp.rm-n4
vector
the product of the matrix q6_sh.rm-n4 and the vector q6_denom_ones
q6_sp.rm-n3
vector
the product of the matrix q6_sh.rm-n3 and the vector q6_denom_ones
q6_sp.rm-n2
vector
the product of the matrix q6_sh.rm-n2 and the vector q6_denom_ones
q6_sp.rm-n1
vector
the product of the matrix q6_sh.rm-n1 and the vector q6_denom_ones
q6_sp.rm-0
vector
the product of the matrix q6_sh.rm-0 and the vector q6_denom_ones
q6_sp.rm-p1
vector
the product of the matrix q6_sh.rm-p1 and the vector q6_denom_ones
q6_sp.rm-p2
vector
the product of the matrix q6_sh.rm-p2 and the vector q6_denom_ones
q6_sp.rm-p3
vector
the product of the matrix q6_sh.rm-p3 and the vector q6_denom_ones
q6_sp.rm-p4
vector
the product of the matrix q6_sh.rm-p4 and the vector q6_denom_ones
q6_sp.rm-p5
vector
the product of the matrix q6_sh.rm-p5 and the vector q6_denom_ones
q6_sp.rm-p6
vector
the product of the matrix q6_sh.rm-p6 and the vector q6_denom_ones
q6_sp.im-n6
vector
the product of the matrix q6_sh.im-n6 and the vector q6_denom_ones
q6_sp.im-n5
vector
the product of the matrix q6_sh.im-n5 and the vector q6_denom_ones
q6_sp.im-n4
vector
the product of the matrix q6_sh.im-n4 and the vector q6_denom_ones
q6_sp.im-n3
vector
the product of the matrix q6_sh.im-n3 and the vector q6_denom_ones
q6_sp.im-n2
vector
the product of the matrix q6_sh.im-n2 and the vector q6_denom_ones
q6_sp.im-n1
vector
the product of the matrix q6_sh.im-n1 and the vector q6_denom_ones
q6_sp.im-0
vector
the product of the matrix q6_sh.im-0 and the vector q6_denom_ones
q6_sp.im-p1
vector
the product of the matrix q6_sh.im-p1 and the vector q6_denom_ones
q6_sp.im-p2
vector
the product of the matrix q6_sh.im-p2 and the vector q6_denom_ones
q6_sp.im-p3
vector
the product of the matrix q6_sh.im-p3 and the vector q6_denom_ones
q6_sp.im-p4
vector
the product of the matrix q6_sh.im-p4 and the vector q6_denom_ones
q6_sp.im-p5
vector
the product of the matrix q6_sh.im-p5 and the vector q6_denom_ones
q6_sp.im-p6
vector
the product of the matrix q6_sh.im-p6 and the vector q6_denom_ones: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the label for the matrix and the vector/scalar that are being multiplied
=q6_sh.*,q6_denom_ones
q6_rmn-n6The CUSTOM action with label q6_rmn-n6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-n6
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-n6,q6_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
q6_imn-n6The CUSTOM action with label q6_imn-n6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-n6
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-n6,q6_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
q6_rmn-n5The CUSTOM action with label q6_rmn-n5 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-n5
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-n5,q6_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
q6_imn-n5The CUSTOM action with label q6_imn-n5 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-n5
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-n5,q6_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
q6_rmn-n4The CUSTOM action with label q6_rmn-n4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-n4
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-n4,q6_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
q6_imn-n4The CUSTOM action with label q6_imn-n4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-n4
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-n4,q6_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
q6_rmn-n3The CUSTOM action with label q6_rmn-n3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-n3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-n3,q6_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
q6_imn-n3The CUSTOM action with label q6_imn-n3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-n3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-n3,q6_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
q6_rmn-n2The CUSTOM action with label q6_rmn-n2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-n2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-n2,q6_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
q6_imn-n2The CUSTOM action with label q6_imn-n2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-n2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-n2,q6_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
q6_rmn-n1The CUSTOM action with label q6_rmn-n1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-n1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-n1,q6_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
q6_imn-n1The CUSTOM action with label q6_imn-n1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-n1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-n1,q6_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
q6_rmn-0The CUSTOM action with label q6_rmn-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-0
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-0,q6_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
q6_imn-0The CUSTOM action with label q6_imn-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-0
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-0,q6_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
q6_rmn-p1The CUSTOM action with label q6_rmn-p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-p1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-p1,q6_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
q6_imn-p1The CUSTOM action with label q6_imn-p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-p1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-p1,q6_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
q6_rmn-p2The CUSTOM action with label q6_rmn-p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-p2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-p2,q6_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
q6_imn-p2The CUSTOM action with label q6_imn-p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-p2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-p2,q6_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
q6_rmn-p3The CUSTOM action with label q6_rmn-p3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-p3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-p3,q6_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
q6_imn-p3The CUSTOM action with label q6_imn-p3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-p3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-p3,q6_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
q6_rmn-p4The CUSTOM action with label q6_rmn-p4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-p4
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-p4,q6_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
q6_imn-p4The CUSTOM action with label q6_imn-p4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-p4
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-p4,q6_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
q6_rmn-p5The CUSTOM action with label q6_rmn-p5 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-p5
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-p5,q6_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
q6_imn-p5The CUSTOM action with label q6_imn-p5 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-p5
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-p5,q6_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
q6_rmn-p6The CUSTOM action with label q6_rmn-p6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rmn-p6
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.rm-p6,q6_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
q6_imn-p6The CUSTOM action with label q6_imn-p6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_imn-p6
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_sp.im-p6,q6_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
q6_rms-n6The MEAN action with label q6_rms-n6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-n6
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 values input to this function
=q6_rmn-n6 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-n6The MEAN action with label q6_ims-n6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-n6
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 values input to this function
=q6_imn-n6 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-n5The MEAN action with label q6_rms-n5 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-n5
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 values input to this function
=q6_rmn-n5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-n5The MEAN action with label q6_ims-n5 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-n5
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 values input to this function
=q6_imn-n5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-n4The MEAN action with label q6_rms-n4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-n4
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 values input to this function
=q6_rmn-n4 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-n4The MEAN action with label q6_ims-n4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-n4
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 values input to this function
=q6_imn-n4 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-n3The MEAN action with label q6_rms-n3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-n3
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 values input to this function
=q6_rmn-n3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-n3The MEAN action with label q6_ims-n3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-n3
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 values input to this function
=q6_imn-n3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-n2The MEAN action with label q6_rms-n2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-n2
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 values input to this function
=q6_rmn-n2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-n2The MEAN action with label q6_ims-n2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-n2
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 values input to this function
=q6_imn-n2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-n1The MEAN action with label q6_rms-n1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-n1
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 values input to this function
=q6_rmn-n1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-n1The MEAN action with label q6_ims-n1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-n1
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 values input to this function
=q6_imn-n1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-0The MEAN action with label q6_rms-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-0
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 values input to this function
=q6_rmn-0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-0The MEAN action with label q6_ims-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-0
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 values input to this function
=q6_imn-0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-p1The MEAN action with label q6_rms-p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-p1
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 values input to this function
=q6_rmn-p1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-p1The MEAN action with label q6_ims-p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-p1
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 values input to this function
=q6_imn-p1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-p2The MEAN action with label q6_rms-p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-p2
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 values input to this function
=q6_rmn-p2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-p2The MEAN action with label q6_ims-p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-p2
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 values input to this function
=q6_imn-p2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-p3The MEAN action with label q6_rms-p3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-p3
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 values input to this function
=q6_rmn-p3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-p3The MEAN action with label q6_ims-p3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-p3
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 values input to this function
=q6_imn-p3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-p4The MEAN action with label q6_rms-p4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-p4
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 values input to this function
=q6_rmn-p4 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-p4The MEAN action with label q6_ims-p4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-p4
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 values input to this function
=q6_imn-p4 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-p5The MEAN action with label q6_rms-p5 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-p5
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 values input to this function
=q6_rmn-p5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-p5The MEAN action with label q6_ims-p5 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-p5
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 values input to this function
=q6_imn-p5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_rms-p6The MEAN action with label q6_rms-p6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_rms-p6
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 values input to this function
=q6_rmn-p6 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_ims-p6The MEAN action with label q6_ims-p6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_ims-p6
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 values input to this function
=q6_imn-p6 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_vmean2The COMBINE action with label q6_vmean2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_vmean2
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 
ARG
the values input to this function
=q6_rms-n6,q6_ims-n6,q6_rms-n5,q6_ims-n5,q6_rms-n4,q6_ims-n4,q6_rms-n3,q6_ims-n3,q6_rms-n2,q6_ims-n2,q6_rms-n1,q6_ims-n1,q6_rms-0,q6_ims-0,q6_rms-p1,q6_ims-p1,q6_rms-p2,q6_ims-p2,q6_rms-p3,q6_ims-p3,q6_rms-p4,q6_ims-p4,q6_rms-p5,q6_ims-p5,q6_rms-p6,q6_ims-p6
q6_vmeanThe CUSTOM action with label q6_vmean calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_vmean
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_vmean2 
FUNC
the function you wish to evaluate
=sqrt(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_norm2The COMBINE action with label q6_norm2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_norm2
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 
ARG
the values input to this function
=q6_sp.rm-n6,q6_sp.im-n6,q6_sp.rm-n5,q6_sp.im-n5,q6_sp.rm-n4,q6_sp.im-n4,q6_sp.rm-n3,q6_sp.im-n3,q6_sp.rm-n2,q6_sp.im-n2,q6_sp.rm-n1,q6_sp.im-n1,q6_sp.rm-0,q6_sp.im-0,q6_sp.rm-p1,q6_sp.im-p1,q6_sp.rm-p2,q6_sp.im-p2,q6_sp.rm-p3,q6_sp.im-p3,q6_sp.rm-p4,q6_sp.im-p4,q6_sp.rm-p5,q6_sp.im-p5,q6_sp.rm-p6,q6_sp.im-p6
q6_normThe CUSTOM action with label q6_norm calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_norm
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_norm2 
FUNC
the function you wish to evaluate
=sqrt(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6The CUSTOM action with label q6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_norm,q6_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 --- diff2The MATHEVAL action with label diff2 calculates the following quantities:
 Quantity   
 Type   
 Description  
diff2
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=q6.vmean,refcv.mean 
FUNC
the function you wish to evaluate
=((x-0.0402)/(0.4404-0.0402)-(y-0.2319)/(0.8137-0.2319 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=diff2 
AT
the positions of the wall
=0.05 
KAPPA
the force constant for the wall
=100000 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall2.bias
scalar
the instantaneous value of the bias potential
uwall2.force2
scalar
the instantaneous value of the squared force due to this bias potential

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
ARG
the labels of the values that you would like to print to the file
 
FILE
the name of the file on which to output these quantities
=COLVAR