PLUMED-NEST

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

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

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

DISTANCES
Calculate the distances between multiple piars of atoms 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
The DISTANCES action with label d1 calculates something
DISTANCES
Calculate the distances between multiple piars of atoms 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 that are 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
The DISTANCES action with label metalc calculates something
DISTANCES
Calculate the distances between multiple piars of atoms 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 that are 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
The DISTANCES action with label metalh calculates something
ANGLES
Calculate an angle. 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
the switching function specifies that only those bonds that have a length that is less than a certain threshold are considered
={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
The ANGLES action with label ang calculates something
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
 calculate the mean of all the quantities
             
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d3

The COORDINATIONNUMBER action with label d3 calculates something
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=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

The COMBINE action with label cv calculates something
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
=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
The UPPER_WALLS action with label wall1 calculates something
UWALLS
Add lower walls to a vector of quantities More details
      
DATA
the values you want to restrain
=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
The UWALLS action with label wall2 calculates something
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=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

The LOWER_WALLS action with label wall3 calculates something
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

The EXTERNAL action with label external calculates the following quantities:
 Quantity   
 Description  
external.bias
the instantaneous value of the bias potential
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

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
=500 
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=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

The REWEIGHT_BIAS action with label wbias calculates the following quantities:
 Quantity   
 Description  
wbias.value
the weight to use for this frame to negate the effect the bias
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=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 esimtation
=0.01
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,wbias
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=5000000
  
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 something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=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 esimtation
=0.01
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,wbias,gcv
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=5000000
  
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 something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=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 esimtation
=0.01
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,wbias,g1
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=5000000
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh1
... HISTOGRAM

The HISTOGRAM action with label hh1 calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=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 esimtation
=0.02
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,wbias,g2
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=5000000
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh2
... HISTOGRAM

The HISTOGRAM action with label hh2 calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=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 esimtation
=0.02
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,wbias,g3
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=5000000
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh3
... HISTOGRAM

The HISTOGRAM action with label hh3 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)
=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
The CONVERT_TO_FES action with label ff 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)
=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
The CONVERT_TO_FES action with label ffg 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)
=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
The CONVERT_TO_FES action with label ff1 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)
=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
The CONVERT_TO_FES action with label ff2 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)
=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

The CONVERT_TO_FES action with label ff3 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)
=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 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
=1000000
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)
=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 grid you would like to print (can also use ARG for specifying what is being printed)
=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 grid you would like to print (can also use ARG for specifying what is being printed)
=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