Project ID: plumID:21.009
Source: npt-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
tested onv2.10
tested onmaster
tested on master
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
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
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
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
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
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
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
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
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
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
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