PLUMED-NEST

Project ID: plumID:19.044
Source: MultithermalMultibaricSimulations/MultithermalMultibaric/Input/plumed.start.dat
Originally used with PLUMED version: 2.4-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. 

energyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details

volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box: VOLUMECalculate the volume the simulation box. More details

# Construct a bias potential using VES
#
# Basis functions

bf1: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=10 MINIMUMThe minimum of the interval on which the basis functions are defined=-14750 MAXIMUMThe maximum of the interval on which the basis functions are defined=-12250
The BF_LEGENDRE action with label bf1 calculates somethingbf2: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=10 MINIMUMThe minimum of the interval on which the basis functions are defined=6.5 MAXIMUMThe maximum of the interval on which the basis functions are defined=8.25

# Target distributions
The BF_LEGENDRE action with label bf2 calculates somethingTD_MULTITHERMAL_MULTIBARICMultithermal-multibaric target distribution (dynamic). More details ...
 MIN_TEMPMinimum energy=260
 MAX_TEMPMaximum energy=350
 MAX_PRESSUREMaximum pressure=180.66422571 # 300 MPa
 MIN_PRESSUREMinimum pressure=0.06022140857
 PRESSURETarget pressure of the barostat used in the MD engine=0.06022140857
 STEPS_PRESSURE Number of pressure steps=20
 STEPS_TEMP Number of temperature steps=20
 SIGMAThe standard deviation parameters of the Gaussian kernels used for smoothing the target distribution=50.,0.05
 THRESHOLD Maximum exploration free energy in kT=1
 LABELa label for the action so that its output can be referenced in the input to other actions=td_multi
... TD_MULTITHERMAL_MULTIBARIC

# Expansion

The TD_MULTITHERMAL_MULTIBARIC action with label td_multi calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. This action has hidden defaults. More details ...
 ARGthe labels of the scalars on which the bias will act=energy,vol
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1,bf2
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300.0
 GRID_BINSthe number of bins used for the grid=200,200
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_multi
 LABELa label for the action so that its output can be referenced in the input to other actions=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1.bias
scalar
the instantaneous value of the bias potential
b1.force2
scalar
the instantaneous value of the squared force due to this bias potential.
... VES_LINEAR_EXPANSION
VES_LINEAR_EXPANSIONLinear basis set expansion bias. This action uses the defaults shown here. More details ...
 ARGthe labels of the scalars on which the bias will act=energy,vol
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1,bf2
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300.0
 GRID_BINSthe number of bins used for the grid=200,200
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_multi
 LABELa label for the action so that its output can be referenced in the input to other actions=b1
 GRID_FMT the format to use when outputting the numbers in the grids=%14.9f
... VES_LINEAR_EXPANSION

# Optimization algorithm

OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action has hidden defaults. 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=10. # Later I found a stepsize of 1 seems to work better.
  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=10
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=100
... OPT_AVERAGED_SGD
The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalarOPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action uses the defaults shown here. 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=10. # Later I found a stepsize of 1 seems to work better.
  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=10
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=100
 COEFFS_FILE the name of output file for the coefficients=coeffs.data
... OPT_AVERAGED_SGD

PRINTPrint quantities to a file. More details 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 STRIDE the frequency with which the quantities of interest should be output=500