PLUMED-NEST

Project ID: plumID:20.003
Source: plumed.dat
Originally used with PLUMED version: 2.6-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. 
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=TD_TS-target-plumed2.6.cpp
The LOAD action with label  calculates something
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 somethingbf1: 
BF_LEGENDRE
Legendre polynomials basis functions. More details
 
MINIMUM
The minimum of the interval on which the basis functions are defined
=-3 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=+3 
ORDER
The order of the basis function expansion
=14 
SCALED
 Scale the polynomials such that they are orthonormal to 1
 

The BF_LEGENDRE action with label bf1 calculates something
TD_TS_TARGET
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
  SCALEFACTOR=30
  LAMBDA=0.05    
  LIMIT=0.1
  PRINT_STRIDE=500
  LABEL=td
... TD_TS_TARGET

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
=1.0
  
GRID_BINS
the number of bins used for the grid
=300
  
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td
... 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
=1
  
FES_OUTPUT
how often the FES(s) should be written out to file
=100
  
COEFFS_OUTPUT
 how often the coefficients should be written to file
=100
  
TARGETDIST_OUTPUT
how often the dynamic target distribution(s) should be written out to file
=500
  
TARGETDIST_STRIDE
stride for updating a target distribution that is iteratively updated during the optimization
=500
  
MONITOR_AVERAGE_GRADIENT
 if the averaged gradient should be monitored and quantities related to it should be outputted
... OPT_AVERAGED_SGD

The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalar
o1.avergradrms
the root mean square value of the averaged coefficient gradient
o1.avergradmax
the largest absolute value of the averaged coefficient gradient
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=colvar.data 
FMT
the format that should be used to output real numbers
=%8.4f