PLUMED-NEST

Project ID: plumID:22.031
Source: 2D_Potential/s54/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

p: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1
The POSITION action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the atom position
p.y
the y-component of the atom position
p.z
the z-component of the atom positiondoubleWell: 
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
...
potential: 
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
The BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Description  
potential.bias
the instantaneous value of the bias potential
potential._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filetheta27: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=0.3*pi/2
The CONSTANT action with label theta27 calculates a scalar quantitysx27: 
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
sy27: 
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
theta54: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=0.6*pi/2
The CONSTANT action with label theta54 calculates a scalar quantitysx54: 
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
sy54: 
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
theta90: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=1.0*pi/2
The CONSTANT action with label theta90 calculates a scalar quantitysx90: 
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
sy90: 
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_exc: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=sx54 
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. 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
=sx54
  
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

The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
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
=sx54
 
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