Project ID: plumID:22.025
Source: t0.700/p0.15808-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
tested onv2.9
tested onmaster
tested on master
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=../../code/ReweightGeomFES.cpp
UNITS
This command sets the internal units for the code. More details
NATURAL
use natural units

VOLUME
Calculate the volume of the simulation box. More details
LABEL
a label for the action so that its output can be referenced in the input to other actions
=vol
CUSTOM
Calculate a combination of variables using a custom expression. More details
ARG
the input to this function
=vol
FUNC
the function you wish to evaluate
=x/4096
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
=molvol
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
=1-4096
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=1.6 D_MAX=2.5}
LESS_THAN
calculate the number of variables that are less than a certain target value
={RATIONAL R_0=5 D_MAX=7.5 NN=12}
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
=molvol
AT
the positions of the wall
=1.55
KAPPA
the force constant for the wall
=1e5
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall1
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.lessthan
AT
the positions of the wall
=1e5
KAPPA
the force constant for the wall
=1.0
STRIDE
the frequency with which the forces due to the bias should be calculated
=10
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall2
# ANN BIAS
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
=molvol
NUM_LAYERS
number of layers of the neural network
=4
NUM_NODES
numbers of nodes in each layer of the neural network
=1,1,12,1
ACTIVATIONS
activation functions for the neural network
=Linear,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,
=10.0
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,
=-0.39724672,4.53955482,4.57188519,0.41611828,0.34503041,-0.32008151,2.11203569,-0.3546259,-7.5084896,0.37947159,0.32988717,0.33968741
WEIGHTS2
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,
=1.37865052,-1.37979639,5.89962585,-1.3073785,-0.94821186,0.96025422,-7.96454951,1.40317079,2.83713787,-1.53205714,-1.06645779,-1.48230519
BIASES0
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,
=-14.0
BIASES1
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,
=-0.21596242,0.21255044,-3.96125122,0.12077826,0.5681013,-0.84645546,-3.54714867,-0.49161144,1.17991367,0.31852111,0.72382993,0.62428802
BIASES2
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,
=-0.11206909 ... ANN
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
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
=0.700
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
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
TEMP=0.700 ARG=coord.lessthan 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.lessthan
GRID_MIN
the lower bounds for the grid
=-1
GRID_MAX
the upper bounds for the grid
=20
GRID_BIN
the number of bins for the grid
=1050
BANDWIDTH
the bandwidths for kernel density esimtation
=0.2
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
STRIDE
the frequency with which to store data for averaging
=10
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.lessthan
GRID_MIN
the lower bounds for the grid
=-1
GRID_MAX
the upper bounds for the grid
=20
GRID_BIN
the number of bins for the grid
=1050
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
STRIDE
the frequency with which to store data for averaging
=10
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hhg ... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
...
ARG
the quantity that is being averaged
=molvol
GRID_MIN
the lower bounds for the grid
=1.40
GRID_MAX
the upper bounds for the grid
=1.60
GRID_BIN
the number of bins for the grid
=400
BANDWIDTH
the bandwidths for kernel density esimtation
=0.005
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
=hhd ... 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
=0.700
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
=0.700
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ffg
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)
=hhd
TEMP
the temperature at which you are operating
=0.700
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ffd
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
=2000000
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
=2000000
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)
=ffd
FILE
the file on which to write the grid
=fesd
STRIDE
the frequency with which the grid should be output to the file
=2000000
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
=2000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=molvol,coord.lessthan,b1.bias
STRIDE
the frequency with which the quantities of interest should be output
=200
FILE
the name of the file on which to output these quantities
=colvar