PLUMED-NEST-TEST-SITE

Project ID: plumID:21.013
Source: ch4-base/bend-param/plumed.inp
Originally used with PLUMED version: 2.6
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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs ENERGYthe units of energy=kcal/mol

The UNITS action with label  calculates somethingANGLESCalculate functions of the distribution of angles. This action is a shortcut. More details GROUPAA group of central atoms about which angles should be calculated=1 GROUPBWhen used in conjunction with GROUPA this keyword instructs plumed to calculate all distinct angles involving one atom from GROUPA and two atoms from GROUPB=2-5 BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=0.5pi UPPER=0.7pi} SWITCHthe switching function specifies that only those bonds that have a length that is less than a certain threshold are considered={RATIONAL D_0=1.50 R_0=0.25} LABELa label for the action so that its output can be referenced in the input to other actions=angThe ANGLES action with label ang calculates the following quantities:
 Quantity   
 Type   
 Description  
ang_between
scalar
the number of colvars that have a value that lies in a particular interval
# PLUMED interprets the command:
# ANGLES GROUPA=1 GROUPB=2-5 BETWEEN={GAUSSIAN LOWER=0.5pi UPPER=0.7pi} SWITCH={RATIONAL D_0=1.50 R_0=0.25} LABEL=ang
# as follows (Click the red comment above to revert to the short version of the input):
The ANGLES action with label ang calculates the following quantities:
 Quantity   
 Description  
ang.value
the ANGLE for each set of three atoms that were specified
ang.between
the number of colvars that have a value that lies in a particular intervalang: COORD_ANGLESCalculate functions of the distribution of angles between bonds in the first coordination spheres of a set of atoms More details SWITCHthe switching function specifies that only those bonds that have a length that is less than a certain threshold are considered={RATIONAL D_0=1.50 R_0=0.25} CATOMSall the angles between the bonds that radiate out from these central atom are computed=1 GROUPa list of angls between pairs of bonds connecting one of the atoms specified using the CATOM command and two of the atoms specified here are computed=2-5  BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=0.5pi UPPER=0.7pi}
# --- End of included input --- 
bf1: BF_CHEBYSHEVChebyshev polynomial basis functions. More details MINIMUMThe minimum of the interval on which the basis functions are defined=1.0 MAXIMUMThe maximum of the interval on which the basis functions are defined=4.5 ORDERThe order of the basis function expansion=96

The BF_CHEBYSHEV action with label bf1 calculates somethingtd: TD_GRIDTarget distribution from an external grid file (static). More details FILEThe name of the external grid file to be used as a target distribution=histo

# Expansion

The TD_GRID action with label td 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=ang.between
 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=500
 GRID_BINSthe number of bins used for the grid=3500
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
 LABELa label for the action so that its output can be referenced in the input to other actions=externalThe VES_LINEAR_EXPANSION action with label external calculates the following quantities:
 Quantity   
 Type   
 Description  
external.bias
scalar
the instantaneous value of the bias potential
external.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=ang.between
 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=500
 GRID_BINSthe number of bins used for the grid=3500
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
 LABELa label for the action so that its output can be referenced in the input to other actions=external
 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=external
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=5000
  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=0.5
  FES_OUTPUThow often the FES(s) should be written out to file=10000
  BIAS_OUTPUThow often the bias(es) should be written out to file=100
  FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file=20
  COEFFS_OUTPUT how often the coefficients should be written to file=1
... 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=external
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=5000
  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=0.5
  FES_OUTPUThow often the FES(s) should be written out to file=10000
  BIAS_OUTPUThow often the bias(es) should be written out to file=100
  FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file=20
  COEFFS_OUTPUT how often the coefficients should be written to file=1
 COEFFS_FILE the name of output file for the coefficients=coeffs.data
... OPT_AVERAGED_SGD

FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=100000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ang.between,external.bias STRIDE the frequency with which the quantities of interest should be output=10000 FILEthe name of the file on which to output these quantities=colvar