PLUMED-NEST

Project ID: plumID:20.010
Source: BiasedSimulations/96molecules/280K/plumed.start.dat
Originally used with PLUMED version: 2.6-dev
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. 

vol: VOLUMECalculate the volume the simulation box. More details

The VOLUME action with label vol calculates the volume of simulation boxENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. More details ...
 SPECIESthis keyword is used for colvars such as coordination number=1-288:3
 SIGMA the width to use for the gaussian kernels=0.055
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv
 REFERENCE_1PDB files with relative distances from central atom=../../../Environments/IceIhExtendedEnvironments/env1.pdb
 REFERENCE_2PDB files with relative distances from central atom=../../../Environments/IceIhExtendedEnvironments/env2.pdb
 REFERENCE_3PDB files with relative distances from central atom=../../../Environments/IceIhExtendedEnvironments/env3.pdb
 REFERENCE_4PDB files with relative distances from central atom=../../../Environments/IceIhExtendedEnvironments/env4.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.5 NN=12 MM=24}
 MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

# Construct a bias potential using VES
#
# Basis functions

The ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:
 Quantity   
 Description  
refcv.value
the environmental similar parameter for each of the input atoms
refcv.morethan
the number of colvars that have a value more than a threshold
refcv.mean
the mean of the colvarsbf1: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=20 MINIMUMThe minimum of the interval on which the basis functions are defined=0.0 MAXIMUMThe maximum of the interval on which the basis functions are defined=96.0

# Target distribution

The BF_LEGENDRE action with label bf1 calculates somethingtd_welltemp: TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More details BIASFACTORThe bias factor used for the well-tempered distribution=50

# Expansion

The TD_WELLTEMPERED action with label td_welltemp calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. More details ...
 ARGthe labels of the scalars on which the bias will act=refcv.morethan
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=280.0
 GRID_BINSthe number of bins used for the grid=300
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_welltemp
 LABELa label for the action so that its output can be referenced in the input to other actions=b1
... VES_LINEAR_EXPANSION

# Optimization algorithm

The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1.force2
the instantaneous value of the squared force due to this bias potentialOPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. More details ...
  BIASthe label of the VES bias to be optimized=b1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=500
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  STEPSIZEthe step size used for the optimization=2.
  FES_OUTPUThow often the FES(s) should be written out to file=500
  BIAS_OUTPUThow often the bias(es) should be written out to file=500
  TARGETDIST_OUTPUThow often the dynamic target distribution(s) should be written out to file=500
  COEFFS_OUTPUT how often the coefficients should be written to file=100
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=500
  #MULTIPLE_WALKERS
... OPT_AVERAGED_SGD

The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalarENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. More details ...
 SPECIESthis keyword is used for colvars such as coordination number=1-288:3
 SIGMA the width to use for the gaussian kernels=0.055
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv2
 REFERENCE_1PDB files with relative distances from central atom=../../../Environments/IceIcExtendedEnvironments/env1.pdb
 REFERENCE_2PDB files with relative distances from central atom=../../../Environments/IceIcExtendedEnvironments/env2.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.5 NN=12 MM=24}
 MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

The ENVIRONMENTSIMILARITY action with label refcv2 calculates the following quantities:
 Quantity   
 Description  
refcv2.value
the environmental similar parameter for each of the input atoms
refcv2.morethan
the number of colvars that have a value more than a threshold
refcv2.mean
the mean of the colvarsdiff: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=refcv2.mean,refcv.mean FUNCthe function you wish to evaluate=((x-0.26)/(0.58-0.26)-(y-0.29)/(0.80-0.29)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label diff calculates the following quantities:
 Quantity   
 Description  
diff.value
an arbitrary functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff ATthe positions of the wall=0.04 KAPPAthe force constant for the wall=100000 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall

# Avoid other structures
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialQ6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-288:3 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.3 D_MAX=0.35} VMEAN calculate the norm of the mean vector LABELa 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._vmean
the norm of the mean vector
q6.value
the norms of the vectors of spherical harmonic coefficientsdiff2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=q6.vmean,refcv.mean FUNCthe function you wish to evaluate=((x-0.0668781995)/(0.39184059-0.0668781995)-(y-0.2899390548628429)/(0.7838534089775562-0.2899390548628429)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


The MATHEVAL action with label diff2 calculates the following quantities:
 Quantity   
 Description  
diff2.value
an arbitrary functionPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR