PLUMED-NEST

Project ID: plumID:20.018
Source: da-wt/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

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
=../src/bias/ReweightGeomFES.cpp

DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,3 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d2
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3,4 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d3
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=4,5 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d4
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,6 
LABEl
a label for the action so that its output can be referenced in the input to other actions
=d5
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,6 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d6

The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atoms
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5 
D_0
 The d_0 parameter of the switching function
=1.0 
R_0
The r_0 parameter of the switching function
=1.0 
NN
 The n parameter of the switching function 
=1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn1
The COORDINATION action with label cn1 calculates the following quantities:
 Quantity   
 Description  
cn1.value
the value of the coordination
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=6 
D_0
 The d_0 parameter of the switching function
=1.0 
R_0
The r_0 parameter of the switching function
=1.0 
NN
 The n parameter of the switching function 
=1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn2

The COORDINATION action with label cn2 calculates the following quantities:
 Quantity   
 Description  
cn2.value
the value of the coordination
DENSITY
Depreciated command that is bascially equivalant to GROUP. More details
 
SPECIES
the atoms in the group
=5,6 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ethylene
The DENSITY action with label ethylene calculates something
DENSITY
Depreciated command that is bascially equivalant to GROUP. More details
 
SPECIES
the atoms in the group
=1-4 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=diene

The DENSITY action with label diene calculates something
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1-4 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=mol1
The CENTER action with label mol1 calculates something
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5-6 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=mol2

The CENTER action with label mol2 calculates something
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 ...
  
ATOMS
the atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)
=ethylene,diene
  
SWITCH11
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL D_0=0.0 R_0=2.65}
  
SWITCH12
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL D_0=0.0 R_0=2.65}
  
SWITCH22
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL D_0=0.0 R_0=2.65}
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=mat1
... CONTACT_MATRIX

The CONTACT_MATRIX action with label mat1 calculates something
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 ...
  
ATOMS
the atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)
=ethylene,diene
  
SWITCH11
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL D_0=0.0 R_0=2.12 NN=24}
  
SWITCH12
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL D_0=0.0 R_0=2.12 NN=24}
  
SWITCH22
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL D_0=0.0 R_0=2.12 NN=24}
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=mat2
... CONTACT_MATRIX

The CONTACT_MATRIX action with label mat2 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
=ethylene 
SPECIESB
this keyword is used for colvars such as the coordination number
=diene 
MEAN
 calculate the mean of all the quantities
 
SWITCH
the switching function that it used in the construction of the contact matrix
={GAUSSIAN D_0=1.8 R_0=0.3} 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn

The COORDINATIONNUMBER action with label cn calculates something
SPRINT
Calculate SPRINT topological variables from an adjacency matrix. More details
 
MATRIX
the matrix that you would like to perform SPRINT on
=mat1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ss1
The SPRINT action with label ss1 calculates something
SPRINT
Calculate SPRINT topological variables from an adjacency matrix. More details
 
MATRIX
the matrix that you would like to perform SPRINT on
=mat2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ss2
The SPRINT action with label ss2 calculates something
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=mol1,mol2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dist
The DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Description  
dist.value
the DISTANCE between this pair of atoms
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1,d2,d3,d4,d6 
COEFFICIENTS
 the coefficients of the arguments in your function
=-0.05,0.21,-0.08,0.69,0.69 
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
=hlda
The COMBINE action with label hlda calculates something
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cn1,cn2 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.5,0.5 
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
=simple
The COMBINE action with label simple calculates something
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=ss1.coord-0,ss1.coord-1 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.5,0.5 
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
=sprnt1
The COMBINE action with label sprnt1 calculates something
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=ss2.coord-0,ss2.coord-1 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.5,0.5 
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
=sprnt2

The COMBINE action with label sprnt2 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
=d4,d6 
AT
the positions of the wall
=5.0,5.0 
KAPPA
the force constant for the wall
=50,50 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=walls
The UPPER_WALLS action with label walls 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
=dist,sprnt1,sprnt2,cn.mean,simple 
AT
the positions of the wall
=0,0,0,0,0 
KAPPA
the force constant for the wall
=50,50,50,50,50 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fake

The LOWER_WALLS action with label fake calculates something
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
=hlda
  
SIGMA
the widths of the Gaussian hills
=0.15
  
HEIGHT
the heights of the Gaussian hills
=1.0
  
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
=600
  
GRID_MIN
the lower bounds for the grid
=1.0
  
GRID_MAX
the upper bounds for the grid
=9.0
  
GRID_BIN
the number of bins for the grid
=1600
  
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
  
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=YES
  
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_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details
    
ARG
 the biases that must be taken into account when reweighting
=b1.bias 
TEMP
the system temperature
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bias
The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the bias
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=d4      TEMP=600 LABEL=gd4
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=hlda    TEMP=600 LABEL=ghlda
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=sprnt1  TEMP=600 LABEL=gsprnt1
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=sprnt2  TEMP=600 LABEL=gsprnt2
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=cn.mean TEMP=600 LABEL=gcn
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=simple  TEMP=600 LABEL=gsimple
REWEIGHT_GEOMFES
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=d4,d6   TEMP=600 LABEL=g2d

HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=d4         
GRID_MIN
 the lower bounds for the grid
=1.0 
GRID_MAX
 the upper bounds for the grid
=6.0         
GRID_BIN
the number of bins for the grid
=2000    
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02      
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hd4
The HISTOGRAM action with label hd4 calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=hlda       
GRID_MIN
 the lower bounds for the grid
=1.0 
GRID_MAX
 the upper bounds for the grid
=9.0         
GRID_BIN
the number of bins for the grid
=4000    
BANDWIDTH
the bandwidths for kernel density esimtation
=0.01      
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hhlda
The HISTOGRAM action with label hhlda calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=sprnt1     
GRID_MIN
 the lower bounds for the grid
=0.0 
GRID_MAX
 the upper bounds for the grid
=4.0         
GRID_BIN
the number of bins for the grid
=2000    
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02      
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hsprnt1
The HISTOGRAM action with label hsprnt1 calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=sprnt2     
GRID_MIN
 the lower bounds for the grid
=-0.1 
GRID_MAX
 the upper bounds for the grid
=2.4        
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 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hsprnt2
The HISTOGRAM action with label hsprnt2 calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=simple     
GRID_MIN
 the lower bounds for the grid
=0.1 
GRID_MAX
 the upper bounds for the grid
=0.8         
GRID_BIN
the number of bins for the grid
=3500    
BANDWIDTH
the bandwidths for kernel density esimtation
=0.001     
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hsimple
The HISTOGRAM action with label hsimple calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=d4,d6      
GRID_MIN
 the lower bounds for the grid
=1.0,1.0 
GRID_MAX
 the upper bounds for the grid
=2.0,2.0 
GRID_BIN
the number of bins for the grid
=100,100 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.04,0.04 
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=h2db
The HISTOGRAM action with label h2db calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=d4,d6      
GRID_MIN
 the lower bounds for the grid
=2.0,2.0 
GRID_MAX
 the upper bounds for the grid
=6.0,6.0 
GRID_BIN
the number of bins for the grid
=80,80   
BANDWIDTH
the bandwidths for kernel density esimtation
=0.20,0.20 
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=h2dd
The HISTOGRAM action with label h2dd calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=d4,d6      
GRID_MIN
 the lower bounds for the grid
=2.0,2.0 
GRID_MAX
 the upper bounds for the grid
=2.2,2.2 
GRID_BIN
the number of bins for the grid
=100,100 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02 
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=h2d
The HISTOGRAM action with label h2d calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=d4         
GRID_MIN
 the lower bounds for the grid
=1.0 
GRID_MAX
 the upper bounds for the grid
=6.0         
GRID_BIN
the number of bins for the grid
=2000    
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02      
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,gd4     
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hd4g
The HISTOGRAM action with label hd4g calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=hlda       
GRID_MIN
 the lower bounds for the grid
=1.0 
GRID_MAX
 the upper bounds for the grid
=9.0         
GRID_BIN
the number of bins for the grid
=4000    
BANDWIDTH
the bandwidths for kernel density esimtation
=0.01      
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,ghlda   
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hhldag
The HISTOGRAM action with label hhldag calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=sprnt1     
GRID_MIN
 the lower bounds for the grid
=0.0 
GRID_MAX
 the upper bounds for the grid
=4.0         
GRID_BIN
the number of bins for the grid
=2000    
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02      
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,gsprnt1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hsprnt1g
The HISTOGRAM action with label hsprnt1g calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=sprnt2     
GRID_MIN
 the lower bounds for the grid
=-0.1 
GRID_MAX
 the upper bounds for the grid
=2.4        
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,gsprnt2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hsprnt2g
The HISTOGRAM action with label hsprnt2g calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=simple     
GRID_MIN
 the lower bounds for the grid
=0.1 
GRID_MAX
 the upper bounds for the grid
=0.8         
GRID_BIN
the number of bins for the grid
=3500    
BANDWIDTH
the bandwidths for kernel density esimtation
=0.001     
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,gsimple 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hsimpleg
The HISTOGRAM action with label hsimpleg calculates something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantity that is being averaged
=d4,d6      
GRID_MIN
 the lower bounds for the grid
=2.0,2.0 
GRID_MAX
 the upper bounds for the grid
=2.2,2.2 
GRID_BIN
the number of bins for the grid
=100,100 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02 
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias,g2d     
LABEL
a label for the action so that its output can be referenced in the input to other actions
=h2dg

The HISTOGRAM action with label h2dg 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)
=hd4       
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fd4
The CONVERT_TO_FES action with label fd4 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)
=hhlda     
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fhlda
The CONVERT_TO_FES action with label fhlda 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)
=hsprnt1   
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fsprnt1
The CONVERT_TO_FES action with label fsprnt1 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)
=hsprnt2   
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fsprnt2
The CONVERT_TO_FES action with label fsprnt2 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)
=hsimple   
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fsimple
The CONVERT_TO_FES action with label fsimple 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)
=h2db      
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=f2db
The CONVERT_TO_FES action with label f2db 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)
=h2dd      
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=f2dd
The CONVERT_TO_FES action with label f2dd 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)
=h2d       
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=f2d
The CONVERT_TO_FES action with label f2d 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)
=hd4g       
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fd4g
The CONVERT_TO_FES action with label fd4g 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)
=hhldag     
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fhldag
The CONVERT_TO_FES action with label fhldag 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)
=hsprnt1g   
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fsprnt1g
The CONVERT_TO_FES action with label fsprnt1g 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)
=hsprnt2g   
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fsprnt2g
The CONVERT_TO_FES action with label fsprnt2g 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)
=hsimpleg   
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fsimpleg
The CONVERT_TO_FES action with label fsimpleg 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)
=h2dg       
TEMP
the temperature at which you are operating
=600 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=f2dg

The CONVERT_TO_FES action with label f2dg 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)
=fd4     
FILE
 the file on which to write the grid
=fesd4     
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fhlda   
FILE
 the file on which to write the grid
=feshlda   
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fsprnt1 
FILE
 the file on which to write the grid
=fessprnt1 
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fsprnt2 
FILE
 the file on which to write the grid
=fessprnt2 
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fsimple 
FILE
 the file on which to write the grid
=fessimple 
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=f2db    
FILE
 the file on which to write the grid
=fes2db    
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=f2dd    
FILE
 the file on which to write the grid
=fes2dd    
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=f2d     
FILE
 the file on which to write the grid
=fes2d     
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fd4g     
FILE
 the file on which to write the grid
=fesd4g     
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fhldag   
FILE
 the file on which to write the grid
=feshldag   
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fsprnt1g 
FILE
 the file on which to write the grid
=fessprnt1g 
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fsprnt2g 
FILE
 the file on which to write the grid
=fessprnt2g 
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=fsimpleg 
FILE
 the file on which to write the grid
=fessimpleg 
STRIDE
 the frequency with which the grid should be output to the file
=5000000
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)
=f2dg     
FILE
 the file on which to write the grid
=fes2dg     
STRIDE
 the frequency with which the grid should be output to the file
=5000000

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
=2000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d4,d6,hlda,dist,cn.mean,sprnt1,sprnt2,b1.bias,b1.rct 
STRIDE
 the frequency with which the quantities of interest should be output
=200 
FILE
the name of the file on which to output these quantities
=colvar