PLUMED-NEST

Project ID: plumID:20.018
Source: dimer/plumed.inp
Originally used with PLUMED version: 2.6-mod
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
 
NATURAL
 use natural units

The UNITS action with label  calculates something
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../src/bias/ReweightGeomFES.cpp

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
The DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Description  
dist.value
the DISTANCE between this pair of atoms
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=2 
R_0
The r_0 parameter of the switching function
=1.0 
D_0
 The d_0 parameter of the switching function
=0.75 
NN
 The n parameter of the switching function 
=1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=coord

The COORDINATION action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.value
the value of the coordination
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

The UPPER_WALLS action with label walls calculates something
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=coord
  
SIGMA
the widths of the Gaussian hills
=0.01
  
HEIGHT
the heights of the Gaussian hills
=0.25
  
PACE
the frequency for hill addition
=2500
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10
  
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=1.5
  
GRID_MIN
the lower bounds for the grid
=0.0
  
GRID_MAX
the upper bounds for the grid
=1.0
  
GRID_BIN
the number of bins for the grid
=500
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  
RCT_USTRIDE
the update stride for calculating the c(t) reweighting factor
=1
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=b1
... METAD

The METAD action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
b1.rct
the reweighting factor c(t)
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details
 
TEMP
the system temperature
=1.5 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bias
The REWEIGHT_METAD action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the metadynamics bias
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 TEMP=1.5 ARG=coord LABEL=geom

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
=10.0
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.05
  
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
=hdist
... HISTOGRAM

The HISTOGRAM action with label hdist calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=coord
  
GRID_MIN
 the lower bounds for the grid
=0.0
  
GRID_MAX
 the upper bounds for the grid
=1.0
  
GRID_BIN
the number of bins for the grid
=200
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02
  
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
=hcoord
... HISTOGRAM

The HISTOGRAM action with label hcoord calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=coord
  
GRID_MIN
 the lower bounds for the grid
=0.0
  
GRID_MAX
 the upper bounds for the grid
=1.0
  
GRID_BIN
the number of bins for the grid
=200
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,geom
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hcoordg
... HISTOGRAM

The HISTOGRAM action with label hcoordg calculates something
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)
=hdist 
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
=fdist
The CONVERT_TO_FES action with label fdist calculates something
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)
=hcoord 
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
=fcoord
The CONVERT_TO_FES action with label fcoord calculates something
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)
=hcoordg 
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
=fcoordg

The CONVERT_TO_FES action with label fcoordg calculates something
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)
=fdist 
FILE
 the file on which to write the grid
=fesdist 
STRIDE
 the frequency with which the grid should be output to the file
=500000
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)
=fcoord 
FILE
 the file on which to write the grid
=fescoord 
STRIDE
 the frequency with which the grid should be output to the file
=500000
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)
=fcoordg 
FILE
 the file on which to write the grid
=fescoordg 
STRIDE
 the frequency with which the grid should be output to the file
=500000

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,coord,b1.bias,b1.rct 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=colvar