PLUMED-NEST

Project ID: plumID:22.025
Source: p0.026/t0.8675-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

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../../code/ReweightGeomFES.cpp
 
The LOAD action with label  calculates something
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
The VOLUME action with label vol calculates the following quantities:
 Quantity   
 Description  
vol.value
the volume of simulation box
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=vol 
FUNC
the function you wish to evaluate
=x/17576 
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

The CUSTOM action with label molvol calculates the following quantities:
 Quantity   
 Description  
molvol.value
an arbitrary function
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
=1-17576
  
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

The COORDINATIONNUMBER action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.lessthan
the number of colvars that have a value less than a threshold
coord.value
the coordination numbers of the specified atoms
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
=1.95 
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
The UPPER_WALLS action with label wall1 calculates the following quantities:
 Quantity   
 Description  
wall1.bias
the instantaneous value of the bias potential
wall1.force2
the instantaneous value of the squared force due to this bias potential
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
=200 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall2

# ANN BIAS
The UPPER_WALLS action with label wall2 calculates the following quantities:
 Quantity   
 Description  
wall2.bias
the instantaneous value of the bias potential
wall2.force2
the instantaneous value of the squared force due to this bias potential
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 labels of the values from which the function is calculated
=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, 
=2.46926878,0.05613827,3.01790344,2.40491131,0.61211034,-5.49143851,1.25682086,-0.36173004,-1.5818871,1.29743407,0.29723546,1.20006447
  
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, 
=-3.66710837,-0.73038555,3.75775896,-3.99676659,-0.96607881,1.38706878,-2.13310274,1.26209618,1.17803885,-1.90685947,-0.95995672,-1.47064834
  
BIASES0
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, 
=-18.0
  
BIASES1
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, 
=-3.08499206,0.9598233,-2.68039101,-4.65895419,0.78752127,0.01424578,-2.42349314,-0.69649879,-1.1142154,1.08788273,0.70221443,1.05279764
  
BIASES2
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, 
=-0.088429
... 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 values 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
The CUSTOM action with label wt calculates the following quantities:
 Quantity   
 Description  
wt.value
an arbitrary function
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the labels of the scalar/vector arguments whose values will be used as a bias on the system
=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
=0.8675 
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 the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the bias
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 TEMP=0.8675 ARG=coord.lessthan LABEL=gd1

HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantities that are being used to construct the histogram
=coord.lessthan
  
GRID_MIN
 the lower bounds for the grid
=0
  
GRID_MAX
 the upper bounds for the grid
=1000
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=10.0
  
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
=200
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh
... HISTOGRAM

The HISTOGRAM action with label hh calculates the following quantities:
 Quantity   
 Description  
hh.value
the estimate of the histogram as a function of the argument that was obtained
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantities that are being used to construct the histogram
=coord.lessthan
  
GRID_MIN
 the lower bounds for the grid
=0
  
GRID_MAX
 the upper bounds for the grid
=1000
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=10.0
  
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
=200
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hhg
... HISTOGRAM

The HISTOGRAM action with label hhg calculates the following quantities:
 Quantity   
 Description  
hhg.value
the estimate of the histogram as a function of the argument that was obtained
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantities that are being used to construct the histogram
=molvol
  
GRID_MIN
 the lower bounds for the grid
=1.6
  
GRID_MAX
 the upper bounds for the grid
=2.2
  
GRID_BIN
the number of bins for the grid
=1200
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.01
  
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

The HISTOGRAM action with label hhd calculates the following quantities:
 Quantity   
 Description  
hhd.value
the estimate of the histogram as a function of the argument that was obtained
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
=0.8675 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ff
The CONVERT_TO_FES action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
the free energy surface
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
=0.8675 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ffg
The CONVERT_TO_FES action with label ffg calculates the following quantities:
 Quantity   
 Description  
ffg.value
the free energy surface
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
=0.8675 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ffd

The CONVERT_TO_FES action with label ffd calculates the following quantities:
 Quantity   
 Description  
ffd.value
the free energy surface
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 labels of the values that you would like to print to the file
=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