PLUMED-NEST

Project ID: plumID:22.031
Source: 2D_Potential/s90/plumed.dat
Originally used with PLUMED version: 2.9
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units

The UNITS action with label  calculates somethingpThe POSITION action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.x
scalar
the x-component of the atom position
p.y
scalar
the y-component of the atom position
p.z
scalar
the z-component of the atom position: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1
doubleWellThe CUSTOM action with label doubleWell calculates the following quantities:
 Quantity   
 Type   
 Description  
doubleWell
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ...
  
FUNC
the function you wish to evaluate
=2*(x^4+y^4-2*x^2-4*y^2+2*x*y+0.8*x+0.1*y+9.28
...
potentialThe BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Type   
 Description  
potential.bias
scalar
the instantaneous value of the bias potential
potential.doubleWell_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named doubleWell: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=doubleWell

#the rotated CVs
theta27The CONSTANT action with label theta27 calculates the following quantities:
 Quantity   
 Type   
 Description  
theta27
scalar
the constant value that was read from the plumed input: 
CONSTANT
Create a constant value that can be passed to actions This action has hidden defaults. More details
 
VALUE
the single number that you would like to store
=0.3*pi/2
theta27: 
CONSTANT
Create a constant value that can be passed to actions This action uses the defaults shown here. More details
 
VALUE
the single number that you would like to store
=0.3*pi/2  
NROWS
 the number of rows in your input matrix
=0 
NCOLS
 the number of columns in your matrix
=0
sx27The CUSTOM action with label sx27 calculates the following quantities:
 Quantity   
 Type   
 Description  
sx27
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y,theta27 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=cos(z)*x-sin(z)*y
sy27The CUSTOM action with label sy27 calculates the following quantities:
 Quantity   
 Type   
 Description  
sy27
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y,theta27 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=sin(z)*x+cos(z)*y
theta54The CONSTANT action with label theta54 calculates the following quantities:
 Quantity   
 Type   
 Description  
theta54
scalar
the constant value that was read from the plumed input: 
CONSTANT
Create a constant value that can be passed to actions This action has hidden defaults. More details
 
VALUE
the single number that you would like to store
=0.6*pi/2
theta54: 
CONSTANT
Create a constant value that can be passed to actions This action uses the defaults shown here. More details
 
VALUE
the single number that you would like to store
=0.6*pi/2  
NROWS
 the number of rows in your input matrix
=0 
NCOLS
 the number of columns in your matrix
=0
sx54The CUSTOM action with label sx54 calculates the following quantities:
 Quantity   
 Type   
 Description  
sx54
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y,theta54 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=cos(z)*x-sin(z)*y
sy54The CUSTOM action with label sy54 calculates the following quantities:
 Quantity   
 Type   
 Description  
sy54
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y,theta54 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=sin(z)*x+cos(z)*y
theta90The CONSTANT action with label theta90 calculates the following quantities:
 Quantity   
 Type   
 Description  
theta90
scalar
the constant value that was read from the plumed input: 
CONSTANT
Create a constant value that can be passed to actions This action has hidden defaults. More details
 
VALUE
the single number that you would like to store
=1.0*pi/2
theta90: 
CONSTANT
Create a constant value that can be passed to actions This action uses the defaults shown here. More details
 
VALUE
the single number that you would like to store
=1.0*pi/2  
NROWS
 the number of rows in your input matrix
=0 
NCOLS
 the number of columns in your matrix
=0
sx90The CUSTOM action with label sx90 calculates the following quantities:
 Quantity   
 Type   
 Description  
sx90
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y,theta90 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=cos(z)*x-sin(z)*y
sy90The CUSTOM action with label sy90 calculates the following quantities:
 Quantity   
 Type   
 Description  
sy90
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y,theta90 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=sin(z)*x+cos(z)*y

chi_excThe CUSTOM action with label chi_exc calculates the following quantities:
 Quantity   
 Type   
 Description  
chi_exc
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=sx90 
FUNC
the function you wish to evaluate
=step(x+0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias
  
ARG
the input for this action is the scalar output from one or more other actions
=sx90
  
TEMP
 temperature
=1
  
FILE
 a file in which the list of all deposited kernels is stored
=Kernels.data
  
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=compressed.Kernels
  
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=compressed.Kernels
  
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=2000
  
PACE
the frequency for kernel deposition
=100
  
SIGMA
 the initial widths of the kernels
=0.05
  
BARRIER
the free energy barrier to be overcome
=10
  
EXCLUDED_REGION
kernels are not deposited when the action provided here has a nonzero value, see example above
=chi_exc
  
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
... OPES_METAD
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opes
  
ARG
the input for this action is the scalar output from one or more other actions
=sx90
  
TEMP
 temperature
=1
  
FILE
 a file in which the list of all deposited kernels is stored
=Kernels.data
  
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=compressed.Kernels
  
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=compressed.Kernels
  
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=2000
  
PACE
the frequency for kernel deposition
=100
  
SIGMA
 the initial widths of the kernels
=0.05
  
BARRIER
the free energy barrier to be overcome
=10
  
EXCLUDED_REGION
kernels are not deposited when the action provided here has a nonzero value, see example above
=chi_exc
  
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
 
COMPRESSION_THRESHOLD
 merge kernels if closer than this threshold, in units of sigma
=1
... OPES_METAD

COMMITTOR
Does a committor analysis. More details
 ...
 #ARG=p.x,p.y
 #BASIN_LL1=1.4,-2.0
 #BASIN_UL1=2.0,-1.4
 
ARG
the input for this action is the scalar output from one or more other actions
=sx90
 
BASIN_LL1
List of lower limits for basin #
=1.6
 
BASIN_UL1
List of upper limits for basin #
=2.0
 
STRIDE
 the frequency with which the CVs are analyzed
=200
... COMMITTOR

PRINT
Print quantities to a file. More details
 
FMT
the format that should be used to output real numbers
=%8.4f 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y,doubleWell,opes.bias,sx27,sy27,sx54,sy54,sx90,sy90

ENDPLUMED
Terminate plumed input. More details