PLUMED-NEST

Project ID: plumID:22.001
Source: ves_md_linearexpansion/1d-double_well/plumed_sym8.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 NATOMS=100000
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units
p: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1
The POSITION action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the atom position
p.y
the y-component of the atom position
p.z
the z-component of the atom positionene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates a scalar quantitytd_uni: 
TD_UNIFORM
Uniform target distribution (static). More details

# Basisset
BF_WAVELETS
Daubechies Wavelets basis functions. More details
 ...
  
ORDER
The order of the basis function expansion
=8
  
MINIMUM
The minimum of the interval on which the basis functions are defined
=-3.0
  
MAXIMUM
The maximum of the interval on which the basis functions are defined
=+3.0
  
TYPE
Specify the wavelet type
=SYMLETS
  
FUNCTION_LENGTH
The domain size of the individual basis functions
=6
  
TAILS_THRESHOLD
The threshold for cutting off tail wavelets as a fraction of the maximum value
=0.01
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bf1
... BF_WAVELETS

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
=p.x
 
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bf1
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=b1
 
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=0.5
 
GRID_BINS
the number of bins used for the grid
=300
 
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_uni
 
OPTIMIZATION_THRESHOLD
Threshold value to turn off optimization of localized basis functions
=0.000001
... VES_LINEAR_EXPANSION

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. 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
=100
  
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
=10
... OPT_AVERAGED_SGD

The OPT_AVERAGED_SGD action with label o1 calculates a scalar quantity
PRINT
Print quantities to a file. More details
 
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.data 
STRIDE
 the frequency with which the quantities of interest should be output
=100