PLUMED-NEST

Project ID: plumID:21.020
Source: droplet/fes/plumed.inp
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

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

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=./ReweightGeomFES.cpp

COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=coord
  
SPECIES
this keyword is used for colvars such as coordination number
=1-512
  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=5.0 D_MAX=10.0}
  
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=5.0 D_MAX=5.5}
  
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER

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
=coord.morethan 
AT
the positions of the wall
=64 
KAPPA
the force constant for the wall
=1.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall

ANN
Calculates the ANN-function. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fesfit
  
ARG
the input for this action is the scalar output from one or more other actions
=coord.morethan
  
NUM_LAYERS
number of layers of the neural network
=3
  
NUM_NODES
numbers of nodes in each layer of the neural network
=1,12,1
  
ACTIVATIONS
activation functions for the neural network
=Tanh,Linear
  
WEIGHTS0
flattened weight arrays connecting adjacent layers, WEIGHTS0 represents flattened weight array connecting layer 0 and layer 1, WEIGHTS1 represents flattened weight array connecting layer 1 and layer 2, 
=0.9058232,-0.90187826,0.3208892,0.37238594,-0.61194702,-0.06594427,1.70867385,-0.31515388,-0.4163217,0.28925027,0.18196869,-0.31543091
  
WEIGHTS1
flattened weight arrays connecting adjacent layers, WEIGHTS0 represents flattened weight array connecting layer 0 and layer 1, WEIGHTS1 represents flattened weight array connecting layer 1 and layer 2, 
=0.60805163,0.35438915,0.08615935,0.34359914,0.18291669,3.01964527,0.38431888,-0.07582409,-0.35502226,0.3090121,0.30355232,-0.43806144
  
BIASES0
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, 
=-1.71557585,-2.35374153,-1.66746451,-2.24434536,-1.54600118,3.66541523,-1.79000195,1.5943394,2.66015844,-1.51256678,-0.0384513,4.48851321
  
BIASES1
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, 
=0.39086608
... ANN

The ANN action with label fesfit calculates the following quantities:
 Quantity   
 Description  
fesfit.node
components of ANN outputs
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=fesfit.node-0 
FUNC
the function you wish to evaluate
=-1.0*x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wt
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=wt 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=b1
The BIASVALUE action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
REWEIGHT_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details
 
TEMP
the system temperature
=80.7 
ARG
 the biases that must be taken into account when reweighting
=b1.bias 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bias
The REWEIGHT_BIAS action with label bias calculates a scalar quantity
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 TEMP=80.7 ARG=coord.morethan LABEL=gd1

HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=coord.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=64
  
GRID_BIN
the number of bins for the grid
=6450
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.2
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh
... HISTOGRAM

HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=coord.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=64
  
GRID_BIN
the number of bins for the grid
=6450
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.2
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,gd1
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hhg
... HISTOGRAM

CONVERT_TO_FES
Convert a histogram to a free energy surface. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh  
TEMP
the temperature at which you are operating
=80.7 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ff
CONVERT_TO_FES
Convert a histogram to a free energy surface. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hhg 
TEMP
the temperature at which you are operating
=80.7 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ffg

DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff  
FILE
 the file on which to write the grid
=fes  
STRIDE
 the frequency with which the grid should be output to the file
=10000000
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ffg 
FILE
 the file on which to write the grid
=fesg 
STRIDE
 the frequency with which the grid should be output to the file
=10000000

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=200000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=coord.morethan,b1.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=2000 
FILE
the name of the file on which to output these quantities
=colvar