PLUMED-NEST-TEST-SITE

Project ID: plumID:22.015
Source: acs.jpcb.2c00131/plumed-bphp-ves.dat
Originally used with PLUMED version: 2.8
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

psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7938,7939,7940,7945
phiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7939,7940,7945,7946

bf: BF_FOURIERFourier basis functions. More details ORDERThe order of the basis function expansion=10 MINIMUMThe minimum of the interval on which the basis functions are defined=-pi MAXIMUMThe maximum of the interval on which the basis functions are defined=+pi

The BF_FOURIER action with label bf calculates somethingtd_uniform: TD_UNIFORMUniform target distribution (static). More details

The TD_UNIFORM action with label td_uniform 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=psi,phi
  BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf
  LABELa label for the action so that its output can be referenced in the input to other actions=varThe VES_LINEAR_EXPANSION action with label var calculates the following quantities:
 Quantity   
 Type   
 Description  
var.bias
scalar
the instantaneous value of the bias potential
var.force2
scalar
the instantaneous value of the squared force due to this bias potential.
  TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300
  TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_uniform
... 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=psi,phi
  BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf
  LABELa label for the action so that its output can be referenced in the input to other actions=var
  TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300
  TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_uniform
 GRID_FMT the format to use when outputting the numbers in the grids=%14.9f
... VES_LINEAR_EXPANSION

OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. More details ...
  BIASthe label of the VES bias to be optimized=var
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=1000
  LABELa label for the action so that its output can be referenced in the input to other actions=opt
  STEPSIZEthe step size used for the optimization=0.1
  COEFFS_FILE the name of output file for the coefficients=coeffs.dat
  BIAS_OUTPUThow often the bias(es) should be written out to file=5000
  FES_OUTPUThow often the FES(s) should be written out to file=5000
  COEFFS_OUTPUT how often the coefficients should be written to file=5000
... OPT_AVERAGED_SGD

The OPT_AVERAGED_SGD action with label opt calculates the following quantities:
 Quantity   
 Description  
opt.value
a scalarPRINTPrint 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=500 FILEthe name of the file on which to output these quantities=colvar-md.dat FMTthe format that should be used to output real numbers=%12.8f