PLUMED-NEST

Project ID: plumID:20.003
Source: plumed.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. 
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=TD_TS-target-plumed2.6.cpp
The LOAD action with label  calculates somethingUNITSThis command sets the internal units for the code. More details NATURAL use natural units
p: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe 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 positionene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingbf1: BF_LEGENDRELegendre polynomials basis functions. More details MINIMUMThe minimum of the interval on which the basis functions are defined=-3 MAXIMUMThe maximum of the interval on which the basis functions are defined=+3 ORDERThe order of the basis function expansion=14 SCALED Scale the polynomials such that they are orthonormal to 1 

The BF_LEGENDRE action with label bf1 calculates somethingTD_TS_TARGETThis action is not part of PLUMED and was included by using a LOAD command More details ...
  SCALEFACTOR=30
  LAMBDA=0.05    
  LIMIT=0.1
  PRINT_STRIDE=500
  LABEL=td
... TD_TS_TARGET

VES_LINEAR_EXPANSIONLinear basis set expansion bias. More details ...
  ARGthe labels of the scalars on which the bias will act=p.x
  BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
  LABELa label for the action so that its output can be referenced in the input to other actions=b1
  TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=1.0
  GRID_BINSthe number of bins used for the grid=300
  TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
... VES_LINEAR_EXPANSION

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=1
  FES_OUTPUThow often the FES(s) should be written out to file=100
  COEFFS_OUTPUT how often the coefficients should be written to file=100
  TARGETDIST_OUTPUThow often the dynamic target distribution(s) should be written out to file=500
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=500
  MONITOR_AVERAGE_GRADIENT if the averaged gradient should be monitored and quantities related to it should be outputted
... OPT_AVERAGED_SGD

The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalar
o1.avergradrms
the root mean square value of the averaged coefficient gradient
o1.avergradmax
the largest absolute value of the averaged coefficient gradientPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* 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.data FMTthe format that should be used to output real numbers=%8.4f