PLUMED-NEST

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

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

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
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
The ENERGY action with label ene calculates something
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

The VOLUME action with label vol calculates the following quantities:
 Quantity   
 Description  
vol.value
the volume of simulation box
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values input to this function
=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
The COMBINE action with label enthalpy calculates the following quantities:
 Quantity   
 Description  
enthalpy.value
a linear compbination
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values input to this function
=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

The COMBINE action with label sh calculates the following quantities:
 Quantity   
 Description  
sh.value
a linear compbination
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
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0} 
MOMENTS
the list of moments that you would like to calculate
=2 
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 the following quantities:
 Quantity   
 Description  
cn.moment
the moments of the distribution
cn.value
the coordination numbers of the specified atoms
Q6
Calculate sixth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-250 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0} 
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
=q6
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6.mean
the mean of the colvars
q6.value
the norms of the vectors of spherical harmonic coefficients
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
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0} 
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
=q6l

The LOCAL_AVERAGE action with label q6l calculates the following quantities:
 Quantity   
 Description  
q6l.mean
the mean of the colvars
q6l.value
the values of the local averages
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
=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

The LOWER_WALLS action with label dummy calculates the following quantities:
 Quantity   
 Description  
dummy.bias
the instantaneous value of the bias potential
dummy.force2
the instantaneous value of the squared force due to this bias potential
PAIRENTROPY
Calculate the KL Entropy from the radial distribution function More details
 ...
  ATOMS=1-250
  
MAXR
the maximum distance to use for the rdf
=6.5
  SIGMA=0.125
  NHIST=130
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ss
... PAIRENTROPY

The PAIRENTROPY action with label ss calculates the following quantities:
 Quantity   
 Description  
ss.value
the KL-entropy that is computed from the radial distribution function
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
  
ARG
the labels of the scalars on which the bias will act
=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

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
=375 
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
 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 quantities that are being used to construct the histogram
=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 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
=hss
The HISTOGRAM action with label hss calculates the following quantities:
 Quantity   
 Description  
hss.value
the estimate of the histogram as a function of the argument that was obtained
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantities that are being used to construct the histogram
=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 esimtation
=0.004 
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
=hq6l
The HISTOGRAM action with label hq6l calculates the following quantities:
 Quantity   
 Description  
hq6l.value
the estimate of the histogram as a function of the argument that was obtained
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantities that are being used to construct the histogram
=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 esimtation
=0.02 
LOGWEIGHTS
the logarithm of the quantity to use as the weights 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
The HISTOGRAM action with label hssg calculates the following quantities:
 Quantity   
 Description  
hssg.value
the estimate of the histogram as a function of the argument that was obtained
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
ARG
the quantities that are being used to construct the histogram
=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 esimtation
=0.004 
LOGWEIGHTS
the logarithm of the quantity to use as the weights 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

The HISTOGRAM action with label hq6lg calculates the following quantities:
 Quantity   
 Description  
hq6lg.value
the estimate of the histogram as a function of the argument that was obtained
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)
=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
The CONVERT_TO_FES action with label fss calculates the following quantities:
 Quantity   
 Description  
fss.value
the free energy surface
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)
=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
The CONVERT_TO_FES action with label fq6l calculates the following quantities:
 Quantity   
 Description  
fq6l.value
the free energy surface
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)
=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
The CONVERT_TO_FES action with label fssg calculates the following quantities:
 Quantity   
 Description  
fssg.value
the free energy surface
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)
=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

The CONVERT_TO_FES action with label fq6lg calculates the following quantities:
 Quantity   
 Description  
fq6lg.value
the free energy surface
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)
=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 grid you would like to print (can also use ARG for specifying what is being printed)
=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 grid you would like to print (can also use ARG for specifying what is being printed)
=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 grid you would like to print (can also use ARG for specifying what is being printed)
=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 labels of the values that you would like to print to the file
=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