PLUMED-NEST

Project ID: plumID:21.009
Source: nvt-fes/plumed.inp
Originally used with PLUMED version: 2.6
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

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

The COORDINATIONNUMBER action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.morethan
the number of colvars that have a value more than a threshold
coord.value
the coordination numbers of the specified atoms
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
=coord1
  
SPECIES
this keyword is used for colvars such as coordination number
=1-512
  
R_0
The r_0 parameter of the switching function
=5.0
  
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=5.0 D_MAX=5.5}
  
MOMENTS
the list of moments that you would like to calculate
=2,3
  
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER

The COORDINATIONNUMBER action with label coord1 calculates the following quantities:
 Quantity   
 Description  
coord1.morethan
the number of colvars that have a value more than a threshold
coord1.moment
the moments of the distribution
coord1.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
=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

The UPPER_WALLS action with label wall calculates the following quantities:
 Quantity   
 Description  
wall.bias
the instantaneous value of the bias potential
wall.force2
the instantaneous value of the squared force due to this bias potential
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
  
ARG
the labels of the scalars on which the bias will act
=coord.morethan
  
SIGMA
the widths of the Gaussian hills
=5000
  
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
  
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.025
  
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=5.000
  
HEIGHT
the heights of the Gaussian hills
=0.5
  
PACE
the frequency for hill addition
=10000
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15
  
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=80.7
  
GRID_MIN
the lower bounds for the grid
=0.0
  
GRID_MAX
the upper bounds for the grid
=140.0
  
GRID_BIN
the number of bins for the grid
=14000
  
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
=40
  
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
=80.7 
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=80.7 ARG=coord.morethan 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.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.2
  
GRID_MAX
 the upper bounds for the grid
=64
  
GRID_BIN
the number of bins for the grid
=6420
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=40000000
  
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.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.2
  
GRID_MAX
 the upper bounds for the grid
=64
  
GRID_BIN
the number of bins for the grid
=6420
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,gd1
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=40000000
  
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
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
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
=80.7 
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
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
=40000000
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
=40000000

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 labels of the values that you would like to print to the file
=coord.morethan,coord1.morethan,coord1.moment-2,coord1.moment-3,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