Project ID: plumID:20.018
Source: na/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
tested onv2.9
tested onmaster
tested on master
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
TIME
the units of time
=fs
ENERGY
the units of energy
=96.485
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=../src/bias/ReweightGeomFES.cpp
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=PairEntropy.cpp
ENERGY
Calculate the total potential energy 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
=ene
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
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=ene,vol
COEFFICIENTS
the coefficients of the arguments in your function
=1.0,1.0/1602176.5
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
=enthalpy
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=enthalpy
COEFFICIENTS
the coefficients of the arguments in your function
=1.0/250
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
=sh
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIES
this keyword is used for colvars such as coordination number
=1-250
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0}
MOMENTS
calculate the moments of the distribution of collective variables
=2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn
Q6
Calculate sixth order Steinhardt parameters. More details
SPECIES
this keyword is used for colvars such as coordination number
=1-250
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0}
MEAN
take the mean of these variables
LABEL
a label for the action so that its output can be referenced in the input to other actions
=q6
LOCAL_AVERAGE
Calculate averages over spherical regions centered on atoms More details
SPECIES
this keyword is used for colvars such as coordination number
=q6
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0}
MEAN
take the mean of these variables
LABEL
a label for the action so that its output can be referenced in the input to other actions
=q6l
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=q6l.mean
AT
the positions of the wall
=0.0
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
=dummy
PAIRENTROPY
This action is not part of PLUMED and was included by using a LOAD command More details
... ATOMS=1-250 MAXR=6.5 SIGMA=0.125 NHIST=130 LABEL=ss ... PAIRENTROPY
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
=sh,ss
SIGMA
the widths of the Gaussian hills
=0.002,0.10
HEIGHT
the heights of the Gaussian hills
=0.025
PACE
the frequency for hill addition
=2500
BIASFACTOR
use well tempered metadynamics and use this bias factor
=30
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=375
GRID_MIN
the lower bounds for the grid
=-1.10,-6.0
GRID_MAX
the upper bounds for the grid
=-0.95,-1.0
GRID_BIN
the number of bins for the grid
=750,500
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
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
=375
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
ARG=ss TEMP=375 LABEL=gss
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
ARG=q6l.mean TEMP=375 LABEL=gq6l
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
ARG
the input for this action is the scalar output from one or more other actions
=ss
GRID_MIN
the lower bounds for the grid
=-6.0
GRID_MAX
the upper bounds for the grid
=-1.0
GRID_BIN
the number of bins for the grid
=1000
BANDWIDTH
the bandwidths for kernel density estimation
=0.02
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hss
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
ARG
the input for this action is the scalar output from one or more other actions
=q6l.mean
GRID_MIN
the lower bounds for the grid
=0.05
GRID_MAX
the upper bounds for the grid
=0.5
GRID_BIN
the number of bins for the grid
=900
BANDWIDTH
the bandwidths for kernel density estimation
=0.004
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hq6l
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
ARG
the input for this action is the scalar output from one or more other actions
=ss
GRID_MIN
the lower bounds for the grid
=-6.0
GRID_MAX
the upper bounds for the grid
=-1.0
GRID_BIN
the number of bins for the grid
=1000
BANDWIDTH
the bandwidths for kernel density estimation
=0.02
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias,gss
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hssg
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
ARG
the input for this action is the scalar output from one or more other actions
=q6l.mean
GRID_MIN
the lower bounds for the grid
=0.05
GRID_MAX
the upper bounds for the grid
=0.5
GRID_BIN
the number of bins for the grid
=900
BANDWIDTH
the bandwidths for kernel density estimation
=0.004
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias,gq6l
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hq6lg
CONVERT_TO_FES
Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More details
GRID
the action that creates the input grid you would like to use
=hss
TEMP
the temperature at which you are operating
=375
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fss
CONVERT_TO_FES
Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More details
GRID
the action that creates the input grid you would like to use
=hq6l
TEMP
the temperature at which you are operating
=375
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fq6l
CONVERT_TO_FES
Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More details
GRID
the action that creates the input grid you would like to use
=hssg
TEMP
the temperature at which you are operating
=375
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fssg
CONVERT_TO_FES
Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More details
GRID
the action that creates the input grid you would like to use
=hq6lg
TEMP
the temperature at which you are operating
=375
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fq6lg
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the action that creates the grid you would like to output
=fss
FILE
the file on which to write the grid
=fesss
STRIDE
the frequency with which the grid should be output to the file
=10000000
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the action that creates the grid you would like to output
=fq6l
FILE
the file on which to write the grid
=fesq6l
STRIDE
the frequency with which the grid should be output to the file
=10000000
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the action that creates the grid you would like to output
=fssg
FILE
the file on which to write the grid
=fesssg
STRIDE
the frequency with which the grid should be output to the file
=10000000
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the action that creates the grid you would like to output
=fq6lg
FILE
the file on which to write the grid
=fesq6lg
STRIDE
the frequency with which the grid should be output to the file
=10000000
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
=50000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=sh,ss,q6l.mean,b1.bias,b1.rct
STRIDE
the frequency with which the quantities of interest should be output
=50000
FILE
the name of the file on which to output these quantities
=colvar