PLUMED-NEST

Project ID: plumID:20.018
Source: da-tt/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
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values 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 the following quantities:
 Quantity   
 Description  
hlda.value
a linear compbination
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 the following quantities:
 Quantity   
 Description  
walls.bias
the instantaneous value of the bias potential
walls.force2
the instantaneous value of the squared force due to this bias potential
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
=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
=100
  
TTBIASFACTOR
use transition tempered metadynamics with this bias factor
=25
  
CALC_TRANSITION_BIAS
 Set to TRUE if you want to compute a metadynamics transition bias V*(t)
  
TRANSITIONWELL0
This keyword appears multiple times as TRANSITIONWELL followed by an integer
=2.0
  
TRANSITIONWELL1
This keyword appears multiple times as TRANSITIONWELL followed by an integer
=5.0
  
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
  
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)
b1.transbias
the metadynamics transition bias V*(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=hlda    TEMP=600 LABEL=ghlda

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
=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 the following quantities:
 Quantity   
 Description  
hhlda.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
=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 the following quantities:
 Quantity   
 Description  
hhldag.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)
=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 the following quantities:
 Quantity   
 Description  
fhlda.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)
=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 the following quantities:
 Quantity   
 Description  
fhldag.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)
=fhlda   
FILE
 the file on which to write the grid
=feshlda   
STRIDE
 the frequency with which the grid should be output to the file
=500000
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
=500000

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 labels of the values that you would like to print to the file
=d4,d6,hlda,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