Project ID: plumID:21.020
Source: dimer/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
UNITS
This command sets the internal units for the code. More details
NATURAL
use natural units

DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dist
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
=dist
AT
the positions of the wall
=7.0
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
=walls
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
=dist
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,
=-1.10652425,-2.35390282,0.73520869,0.30508303,-1.91710758,-1.17080437,4.54476387,-1.55057519,-0.33438543,-0.51296629,-1.58933892,-0.66991935
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,
=1.12275159,-0.52419477,-1.68730803,0.54981566,-0.50883646,0.39913448,5.41323609,1.35671307,-0.83412662,0.09853493,2.40196946,-3.37362775
BIASES0
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,
=0.92550763,-3.21503713,-2.65645714,-1.50841484,-3.84287814,0.98659592,-5.86437259,1.33560335,2.22786005,0.18571632,1.3609639,5.38428241
BIASES1
bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,
=1.14569644 ... 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
=1.5
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
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
...
ARG
the quantity that is being averaged
=dist
GRID_MIN
the lower bounds for the grid
=0.0
GRID_MAX
the upper bounds for the grid
=8.0
GRID_BIN
the number of bins for the grid
=1600
BANDWIDTH
the bandwidths for kernel density esimtation
=0.1
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
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
=1.5
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ff
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
=1000000
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
=10000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=dist,b1.bias
STRIDE
the frequency with which the quantities of interest should be output
=5000
FILE
the name of the file on which to output these quantities
=colvar