Project ID: plumID:21.002
Source: Crystallization/IceIh/288molecules/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
tested onv2.9
tested onmaster
#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

ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. 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
... ENVIRONMENTSIMILARITY
# Construct a bias potential
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
td_uni:
TD_UNIFORM
Uniform target distribution (static). More details

# Expansion
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
OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. 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
=0.5
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
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. 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
... ENVIRONMENTSIMILARITY
diff:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the 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
=uwall
# Avoid other structures
Q6
Calculate sixth order Steinhardt parameters. 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
=q6 diff2:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the 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
=uwall2
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