PLUMED-NEST-TEST-SITE

Project ID: plumID:21.002
Source: Crystallization/IceIc/64molecules/350K/plumed.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. 

#RESTART

vol: 
VOLUME
Calculate the volume of the simulation box. More details

The VOLUME action with label vol calculates the volume of simulation box
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
=1-192:3
 
SIGMA
 the width to use for the gaussian kernels
=0.050
 
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
=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=8 MM=16}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
The ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:
 Quantity   
 Description  
refcv.morethan
the number of colvars that have a value more than a threshold
refcv.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
=1-192:3
 
SIGMA
 the width to use for the gaussian kernels
=0.050
 
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
=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=8 MM=16}
 
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=1-192:3
#  SIGMA=0.050
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv
#  REFERENCE_1=env1c.pdb
#  REFERENCE_2=env2c.pdb
#  MORE_THAN={RATIONAL R_0=0.5 NN=8 MM=16}
#  MEAN
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
refcv_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
=1-192:3 
CUTOFF
 ignore distances that have a value larger than this cutoff
=0.608629 
The DISTANCE_MATRIX action with label refcv_cmat calculates the following quantities:
 Quantity   
 Description  
refcv_cmat.w
a matrix containing the weights for the bonds between each pair of atoms
refcv_cmat.x
the projection of the bond on the x axis
refcv_cmat.y
the projection of the bond on the y axis
refcv_cmat.z
the projection of the bond on the z axis
refcv_cmat.value
a matrix containing the weights for the bonds between each pair of atomsrefcv_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
=1-192:3 
The GROUP action with label refcv_grp calculates somethingrefcv_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
=64
The ONES action with label refcv_ones calculates the following quantities:
 Quantity   
 Description  
refcv_ones.value
a vector of ones with the required number of elementsrefcv_matenv1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the 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(0.608629-w)/16)*(exp(-((x--0.3243)^2+(y--0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.1622)^2+(y--0.1622)^2+(z-0.1621)^2)/(4*0.0025))+exp(-((x--0.1622)^2+(y-0.1621)^2+(z--0.1622)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3243)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3243)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3242)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3242)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y--0.1622)^2+(z--0.1622)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y-0.1621)^2+(z-0.1621)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y--0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0.3242)^2+(z-0)^2)/(4*0.0025 
The CUSTOM action with label refcv_matenv1 calculates the following quantities:
 Quantity   
 Description  
refcv_matenv1.value
an arbitrary functionrefcv_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
=refcv_matenv1,refcv_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv_env1 calculates the following quantities:
 Quantity   
 Description  
refcv_env1.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv_env1..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv_matenv2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the 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(0.608629-w)/16)*(exp(-((x--0.3243)^2+(y--0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.1621)^2+(y--0.1621)^2+(z--0.1621)^2)/(4*0.0025))+exp(-((x--0.1621)^2+(y-0.1622)^2+(z-0.1622)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3242)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3242)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3243)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3243)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y--0.1621)^2+(z-0.1622)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y-0.1622)^2+(z--0.1621)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y--0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0.3243)^2+(z-0)^2)/(4*0.0025 
The CUSTOM action with label refcv_matenv2 calculates the following quantities:
 Quantity   
 Description  
refcv_matenv2.value
an arbitrary functionrefcv_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
=refcv_matenv2,refcv_ones 
The MATRIX_VECTOR_PRODUCT action with label refcv_env2 calculates the following quantities:
 Quantity   
 Description  
refcv_env2.value
the vector that is obtained by taking the product between the matrix and the vector that were input
refcv_env2..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrefcv: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv_env1,refcv_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 
refcv_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
=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=8 MM=16} 
The MORE_THAN action with label refcv_mt calculates the following quantities:
 Quantity   
 Description  
refcv_mt.value
a function that is one if the if the input is more than a thresholdrefcv_morethan: 
SUM
Calculate the sum of the arguments More details
 
ARG
the 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 
The SUM action with label refcv_morethan calculates the following quantities:
 Quantity   
 Description  
refcv_morethan.value
the sumrefcv_mean: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the 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 using VES
#
# Basis functions

The MEAN action with label refcv_mean calculates the following quantities:
 Quantity   
 Description  
refcv_mean.value
the sumbf1: 
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
=64.0

# 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 input for this action is the scalar output from one or more other actions
=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
=b1
... VES_LINEAR_EXPANSION

# Optimization algorithm

The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1.force2
the instantaneous value of the squared force due to this bias potential
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

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR