PLUMED-NEST

Project ID: plumID:21.032
Source: plumed_fes_1_2.dat
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 
ENERGY
the units of energy
=kcal/mol 
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-781 
STRIDE
 the frequency with which molecules are reassembled
=1



metad:       
READ
Read quantities from a colvar file. More details
 
FILE
the name of the file from which to read these quantities
=COLVAR_REWEIGHT 
IGNORE_TIME
 ignore the time in the colvar file
 
VALUES
the values to read from the file
=metad.bias
The READ action with label metad calculates a scalar quantityweights1: 
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
=300 
ARG
 the biases that must be taken into account when reweighting
=metad.bias


The REWEIGHT_METAD action with label weights1 calculates a scalar quantity
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=67,88,243,292 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn69
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=152,88,324,173 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn68
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=211,292,359,173 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn67
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=465,455,628,434 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn66
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=512,554,465,761 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn65
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=599,424,434,554 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn64
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=751,761,730,628 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn63



zn: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=775-781


Cys: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=67,88,243,292,152,324,173,211,359,465,455,628,434,512,554,761,599,424,751,730



zn69:    
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=781 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn69 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
The COORDINATION action with label zn69 calculates a scalar quantityzn68:    
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=780 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn68 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
The COORDINATION action with label zn68 calculates a scalar quantityzn67:    
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=779 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn67 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
The COORDINATION action with label zn67 calculates a scalar quantityzn66:    
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=778 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn66 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
The COORDINATION action with label zn66 calculates a scalar quantityzn65:    
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=777 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn65 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
The COORDINATION action with label zn65 calculates a scalar quantityzn64:    
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=776 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn64 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
The COORDINATION action with label zn64 calculates a scalar quantityzn63:    
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=775 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn63 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}



The COORDINATION action with label zn63 calculates a scalar quantityzn69_filterbbb: 
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
=781 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn69 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
zn68_filterbbb: 
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
=780 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn68  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}  
zn67_filterbbb: 
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
=779 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn67  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24} 
zn66_filterbbb: 
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
=778 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn66  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
zn65_filterbbb: 
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
=777 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn65  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
zn64_filterbbb: 
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
=776 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn64  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}
zn63_filterbbb: 
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
=775 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn63  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24} 


zn69_filter:    
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
=781 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn69  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}   
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}  
zn68_filter:    
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
=780 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn68  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}    
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}  
zn67_filter:    
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
=779 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn67  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}    
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}  
zn66_filter:    
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
=778 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn66  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}   
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}  
zn65_filter:    
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
=777 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn65 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}     
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24} 
zn64_filter:    
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
=776 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn64  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}    
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24} 
zn63_filter:    
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
=775 
SPECIESB
this keyword is used for colvars such as the coordination number
=comCysZn63  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}    
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24} 



MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=zn69_filterbbb 
SWITCH
the switching function that transform
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}  
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d69  
HIGHEST
 this flag allows you to recover the highest of these variables
 
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=zn68_filterbbb 
SWITCH
the switching function that transform
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}   
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d68 
HIGHEST
 this flag allows you to recover the highest of these variables
  
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=zn67_filterbbb 
SWITCH
the switching function that transform
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}   
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d67 
HIGHEST
 this flag allows you to recover the highest of these variables
 
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=zn66_filterbbb 
SWITCH
the switching function that transform
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}   
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d66 
HIGHEST
 this flag allows you to recover the highest of these variables
  
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=zn65_filterbbb 
SWITCH
the switching function that transform
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}   
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d65 
HIGHEST
 this flag allows you to recover the highest of these variables
  
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=zn64_filterbbb 
SWITCH
the switching function that transform
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}  
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d64 
HIGHEST
 this flag allows you to recover the highest of these variables
 
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=zn63_filterbbb 
SWITCH
the switching function that transform
={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}   
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d63 
HIGHEST
 this flag allows you to recover the highest of these variables
  



Cyss2: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d69.highest,d68.highest,d67.highest,d66.highest,d65.highest,d64.highest,d63.highest   
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO


m: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=zn69_filter.morethan,zn68_filter.morethan,zn67_filter.morethan,zn66_filter.morethan,zn65_filter.morethan,zn64_filter.morethan,zn63_filter.morethan   
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

DRMSD
Calculate the distance RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=reference.pdb 
LOWER_CUTOFF
only pairs of atoms further than LOWER_CUTOFF are considered in the calculation
=0.1 
UPPER_CUTOFF
only pairs of atoms closer than UPPER_CUTOFF are considered in the calculation
=8 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=DRMSD

HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
   
ARG
the quantity that is being averaged
=Cyss2,m
   
GRID_MIN
 the lower bounds for the grid
=0,0
   
GRID_MAX
 the upper bounds for the grid
=30,10
   
BANDWIDTH
the bandwidths for kernel density esimtation
=0.4,0.4
   
GRID_BIN
the number of bins for the grid
=300,300
   
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights1
   
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hB6
   
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=false
... HISTOGRAM


HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
   
ARG
the quantity that is being averaged
=m,DRMSD
   
GRID_MIN
 the lower bounds for the grid
=0,0
   
GRID_MAX
 the upper bounds for the grid
=9,12
   
GRID_BIN
the number of bins for the grid
=300,300
   
BANDWIDTH
the bandwidths for kernel density esimtation
=0.5,0.5
   
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights1
   
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hB5
   
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=false
... HISTOGRAM


fes6: 
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)
=hB6 
TEMP
the temperature at which you are operating
=300
fes5: 
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)
=hB5 
TEMP
the temperature at which you are operating
=300

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)
=hB6 
FILE
 the file on which to write the grid
=histo6.dat 
FMT
the format that should be used to output real numbers
=%8.4f
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)
=hB5 
FILE
 the file on which to write the grid
=histo5.dat 
FMT
the format that should be used to output real numbers
=%8.4f
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)
=fes6 
FILE
 the file on which to write the grid
=fes6.dat 
FMT
the format that should be used to output real numbers
=%8.4f
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)
=fes5 
FILE
 the file on which to write the grid
=fes5.dat 
FMT
the format that should be used to output real numbers
=%8.4f