PLUMED-NEST

Project ID: plumID:22.015
Source: acs.jpcb.2c00131/plumed-bv-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

psi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=25,26,27,32
The TORSION action with label psi calculates a scalar quantityphi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=26,27,32,33

The TORSION action with label phi calculates a scalar quantitybf: 
BF_FOURIER
Fourier basis functions. More details
 
ORDER
The order of the basis function expansion
=10 
MINIMUM
The minimum of the interval on which the basis functions are defined
=-pi 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=+pi

td_uniform: 
TD_UNIFORM
Uniform target distribution (static). More details

VES_LINEAR_EXPANSION
Linear basis set expansion bias. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=psi,phi
  
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bf
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=var
  
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=300
  
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_uniform
... VES_LINEAR_EXPANSION

The VES_LINEAR_EXPANSION action with label var calculates the following quantities:
 Quantity   
 Description  
var.bias
the instantaneous value of the bias potential
var.force2
the instantaneous value of the squared force due to this bias potential
OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. More details
 ...
  
BIAS
the label of the VES bias to be optimized
=var
  
STRIDE
the frequency of updating the coefficients given in the number of MD steps
=1000
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opt
  
STEPSIZE
the step size used for the optimization
=0.1
  
COEFFS_FILE
 the name of output file for the coefficients
=coeffs.dat
  
BIAS_OUTPUT
how often the bias(es) should be written out to file
=5000
  
FES_OUTPUT
how 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 a scalar quantity
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=colvar-md.dat 
FMT
the format that should be used to output real numbers
=%12.8f