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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITSThis 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: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=1
doubleWellThe CUSTOM action with label doubleWell calculates the following quantities:
 Quantity   
 Type   
 Description  
doubleWell
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ...
  FUNCthe 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: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=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: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=0.3*pi/2
theta27: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUEthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y,theta27 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y,theta27 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=0.6*pi/2
theta54: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUEthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y,theta54 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y,theta54 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=1.0*pi/2
theta90: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUEthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y,theta90 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y,theta90 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=sx90 FUNCthe function you wish to evaluate=step(x+0.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  LABELa 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
  ARGthe labels of the scalars on which the bias will act=sx90
  TEMP temperature=1
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=2000
  PACEthe frequency for kernel deposition=100
  SIGMA the initial widths of the kernels=0.05
  BARRIERthe free energy barrier to be overcome=10
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
... OPES_METAD
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes
  ARGthe labels of the scalars on which the bias will act=sx90
  TEMP temperature=1
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=2000
  PACEthe frequency for kernel deposition=100
  SIGMA the initial widths of the kernels=0.05
  BARRIERthe free energy barrier to be overcome=10
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
  RESTARTallows 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

COMMITTORDoes a committor analysis. More details ...
 #ARG=p.x,p.y
 #BASIN_LL1=1.4,-2.0
 #BASIN_UL1=2.0,-1.4
 ARGthe labels of the values which is being used to define the committor surface=sx90
 BASIN_LL1List of lower limits for basin #=1.6
 BASIN_UL1List of upper limits for basin #=2.0
 STRIDE the frequency with which the CVs are analyzed=200
... COMMITTOR

PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%8.4f STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=p.x,p.y,doubleWell,opes.bias,sx27,sy27,sx54,sy54,sx90,sy90

ENDPLUMEDTerminate plumed input. More details