Project ID: plumID:21.013
Source: ch4-diss/ni111-bend/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 onv2.9
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
=kcal/mol
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=../../data/ReweightGeomFES.cpp
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More details
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=66-69
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=65
MAX
calculate the maximum value
={BETA=0.010}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More details
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=65
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=1-64
MIN
calculate the minimum value
={BETA=100.0}
LESS_THAN
calculate the number of variables less than a certain target value
={RATIONAL R_0=2.5}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metalc
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More details
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=66-69
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=1-64
MIN
calculate the minimum value
={BETA=100.0}
LESS_THAN
calculate the number of variables less than a certain target value
={RATIONAL R_0=2.0}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metalh
ANGLES
Calculate functions of the distribution of angles . More details
GROUPA
A group of central atoms about which angles should be calculated
=65
GROUPB
When used in conjunction with GROUPA this keyword instructs plumed to calculate all distinct angles involving one atom from GROUPA and two atoms from GROUPB
=66-69
BETWEEN
calculate the number of values that are within a certain range
={GAUSSIAN LOWER=0.5pi UPPER=0.7pi}
SWITCH
A switching function that ensures that only angles between atoms that are within a certain fixed cutoff are calculated
={RATIONAL D_0=1.50 R_0=0.25}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ang
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=65
SPECIESB
this keyword is used for colvars such as the coordination number
=66-69
R_0
The r_0 parameter of the switching function
=1.75
NN
The n parameter of the switching function
=12
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
=d3
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
=d1.max,metalc.lessthan,metalh.lessthan,ang.between
COEFFICIENTS
the coefficients of the arguments in your function
=0.952,0.225,-0.091,-0.187
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
=cv
UPPER_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
=metalc.min,cv
AT
the positions of the wall
=4.00,5.0
KAPPA
the force constant for the wall
=100,1
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall1
UWALLS
Add ef UPPER_WALLS restraints on all the multicolvar values More details
DATA
certain actions in plumed work by calculating a list of variables and summing over them
=d1
AT
the radius of the sphere
=1.80
KAPPA
the force constant for the wall
=250
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall2
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
=d3.mean,ang.between
AT
the positions of the wall
=2.95,1.25
KAPPA
the force constant for the wall
=1000,1000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall3
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
ARG
the input for this action is the scalar output from one or more other actions
=ang.between
FILE
the name of the file containing the external potential
=extbias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=external
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
=cv
SIGMA
the widths of the Gaussian hills
=0.05
HEIGHT
the heights of the Gaussian hills
=0.25
PACE
the frequency for hill addition
=1000
BIASFACTOR
use well tempered metadynamics and use this bias factor
=25
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=500
GRID_MIN
the lower bounds for the grid
=-3.0
GRID_MAX
the upper bounds for the grid
=3.0
GRID_BIN
the number of bins for the grid
=1200
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
=500
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=500 ARG=cv LABEL=gcv
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
TEMP=500 ARG=d1.max LABEL=g1
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
TEMP=500 ARG=metalc.lessthan LABEL=g2
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
TEMP=500 ARG=ang.between LABEL=g3
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
=500
ARG
the biases that must be taken into account when reweighting
=wall1.bias,wall2.bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wbias
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
=cv
GRID_MIN
the lower bounds for the grid
=-3.0
GRID_MAX
the upper bounds for the grid
=3.0
GRID_BIN
the number of bins for the grid
=6000
BANDWIDTH
the bandwidths for kernel density estimation
=0.01
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias,wbias
CLEAR
the frequency with which to clear all the accumulated data
=5000000
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 input for this action is the scalar output from one or more other actions
=cv
GRID_MIN
the lower bounds for the grid
=-3.0
GRID_MAX
the upper bounds for the grid
=3.0
GRID_BIN
the number of bins for the grid
=6000
BANDWIDTH
the bandwidths for kernel density estimation
=0.01
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias,wbias,gcv
CLEAR
the frequency with which to clear all the accumulated data
=5000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hhg ... HISTOGRAM
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
=d1.max
GRID_MIN
the lower bounds for the grid
=1.0
GRID_MAX
the upper bounds for the grid
=3.5
GRID_BIN
the number of bins for the grid
=2500
BANDWIDTH
the bandwidths for kernel density estimation
=0.01
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias,wbias,g1
CLEAR
the frequency with which to clear all the accumulated data
=5000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh1 ... HISTOGRAM
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
=metalc.lessthan
GRID_MIN
the lower bounds for the grid
=0.0
GRID_MAX
the upper bounds for the grid
=5.0
GRID_BIN
the number of bins for the grid
=2500
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,wbias,g2
CLEAR
the frequency with which to clear all the accumulated data
=5000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh2 ... HISTOGRAM
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
=ang.between
GRID_MIN
the lower bounds for the grid
=1.5
GRID_MAX
the upper bounds for the grid
=4.5
GRID_BIN
the number of bins for the grid
=1500
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,wbias,g3
CLEAR
the frequency with which to clear all the accumulated data
=5000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh3 ... HISTOGRAM
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
=hh
TEMP
the temperature at which you are operating
=500.0
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, 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
=hhg
TEMP
the temperature at which you are operating
=500.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ffg
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
=hh1
TEMP
the temperature at which you are operating
=500.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ff1
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
=hh2
TEMP
the temperature at which you are operating
=500.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ff2
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
=hh3
TEMP
the temperature at which you are operating
=500.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ff3
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
=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
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
=ffg
FILE
the file on which to write the grid
=fesg
STRIDE
the frequency with which the grid should be output to the file
=1000000
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
=ff1
FILE
the file on which to write the grid
=fes1
STRIDE
the frequency with which the grid should be output to the file
=1000000
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
=ff2
FILE
the file on which to write the grid
=fes2
STRIDE
the frequency with which the grid should be output to the file
=1000000
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
=ff3
FILE
the file on which to write the grid
=fes3
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
=100000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=d1.max,metalc.lessthan,metalh.lessthan,ang.between,d3.mean,cv,b1.bias,b1.rct
STRIDE
the frequency with which the quantities of interest should be output
=10000
FILE
the name of the file on which to output these quantities
=colvar