PLUMED-NEST

Project ID: plumID:19.027
Source: MulticanonicalSimulations/Multicanonical/Input/plumed.start.dat
Originally used with PLUMED version: 2.4-dev
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

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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A

The UNITS action with label  calculates somethingenergyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the value calculated by this action: 
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
=20 
MINIMUM
The minimum of the interval on which the basis functions are defined
=-25000 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=-23500

# Target distributions

The BF_LEGENDRE action with label bf1 calculates something
TD_MULTICANONICAL
Multicanonical target distribution (dynamic). More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=td_multi
 
SIGMA
The standard deviation parameters of the Gaussian kernels used for smoothing the target distribution
=50.0
 
MIN_TEMP
Minimum temperature
=400
 
MAX_TEMP
Maximum temperature
=600
 
THRESHOLD
 Maximum exploration free energy in kT
=1
... TD_MULTICANONICAL


# Expansion

The TD_MULTICANONICAL action with label td_multi 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
=energy
 
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
=500.0
 
GRID_BINS
the number of bins used for the grid
=1000
 
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_multi
 
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
  
TARGETDIST_OUTPUT
how often the dynamic target distribution(s) should be written out to file
=500
  
COEFFS_OUTPUT
 how often the coefficients should be written to file
=100
  
TARGETDIST_STRIDE
stride for updating a target distribution that is iteratively updated during the optimization
=500
... 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
  
TARGETDIST_OUTPUT
how often the dynamic target distribution(s) should be written out to file
=500
  
COEFFS_OUTPUT
 how often the coefficients should be written to file
=100
  
TARGETDIST_STRIDE
stride for updating a target distribution that is iteratively updated during the optimization
=500
 
COEFFS_FILE
 the name of output file for the coefficients
=coeffs.data
... OPT_AVERAGED_SGD

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 
STRIDE
 the frequency with which the quantities of interest should be output
=500