PLUMED-NEST

Project ID: plumID:21.013
Source: ch4-base/symm-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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=fs 
ENERGY
the units of energy
=kcal/mol

COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=2 
D_0
 The d_0 parameter of the switching function
=0.85 
R_0
The r_0 parameter of the switching function
=0.25 
NN
 The n parameter of the switching function 
=1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=vib1
The COORDINATION action with label vib1 calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=3 
D_0
 The d_0 parameter of the switching function
=0.85 
R_0
The r_0 parameter of the switching function
=0.25 
NN
 The n parameter of the switching function 
=1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=vib2

The COORDINATION action with label vib2 calculates a scalar quantity
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=2-5 
SPECIESB
this keyword is used for colvars such as the coordination number
=1 
D_0
 The d_0 parameter of the switching function
=0.85 
R_0
The r_0 parameter of the switching function
=0.25 
NN
 The n parameter of the switching function 
=1 
MEAN
take the mean of these variables
 
MOMENTS
calculate the moments of the distribution of collective variables
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=nm

The COORDINATIONNUMBER action with label nm calculates the following quantities:
 Quantity   
 Description  
nm.mean
the mean value
nm.moment
the central moments of the distribution of valuesbf1: 
BF_CHEBYSHEV
Chebyshev polynomial basis functions. More details
 
MINIMUM
The minimum of the interval on which the basis functions are defined
=0.0 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=1.0 
ORDER
The order of the basis function expansion
=96

td: 
TD_GRID
Target distribution from an external grid file (static). More details
 
FILE
The name of the external grid file to be used as a target distribution
=histo

# Expansion

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
=nm.mean
 
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bf1
 
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=500
 
GRID_BINS
the number of bins used for the grid
=2000
 
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=external
... VES_LINEAR_EXPANSION

# Optimization algorithm

The VES_LINEAR_EXPANSION action with label external calculates the following quantities:
 Quantity   
 Description  
external.bias
the instantaneous value of the bias potential
external.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
=external
  
STRIDE
the frequency of updating the coefficients given in the number of MD steps
=5000
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=o1
  
STEPSIZE
the step size used for the optimization
=0.5
  
FES_OUTPUT
how often the FES(s) should be written out to file
=10000
  
BIAS_OUTPUT
how often the bias(es) should be written out to file
=100
  
FES_PROJ_OUTPUT
how 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 a scalar quantity
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=100000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=vib1,vib2,nm.moment-2,nm.mean,external.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=10000 
FILE
the name of the file on which to output these quantities
=colvar