PLUMED-NEST

Project ID: plumID:19.080
Source: h3/fes/plumed.inp
Originally used with PLUMED version: 2.4.1
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

DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1
The DISTANCE action with label d1 calculates a scalar quantity
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,3 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d2
The DISTANCE action with label d2 calculates a scalar quantity
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,3 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d3

The DISTANCE action with label d3 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1,d2 
COEFFICIENTS
 the coefficients of the arguments in your function
=1.0,-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cv
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1,d3 
COEFFICIENTS
 the coefficients of the arguments in your function
=-1.0,1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=block1
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d2,d3 
COEFFICIENTS
 the coefficients of the arguments in your function
=-1.0,1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=block2

UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d1,d2 
AT
the positions of the wall
=2.5,2.5 
KAPPA
the force constant for the wall
=100.0,100.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=constrain
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=block1,block2 
AT
the positions of the wall
=0.0,0.0 
KAPPA
the force constant for the wall
=1000.0,1000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cone
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1 
FILE
the name of the file containing the external potential
=extbias1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=external1
The EXTERNAL action with label external1 calculates the following quantities:
 Quantity   
 Description  
external1.bias
the instantaneous value of the bias potential
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d2 
FILE
the name of the file containing the external potential
=extbias2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=external2

The EXTERNAL action with label external2 calculates the following quantities:
 Quantity   
 Description  
external2.bias
the instantaneous value of the bias potentialbf1: 
BF_CHEBYSHEV
Chebyshev polynomial basis functions. More details
 
MINIMUM
The minimum of the interval on which the basis functions are defined
=-2.5 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=2.5 
ORDER
The order of the basis function expansion
=48

td: 
TD_WELLTEMPERED
Well-tempered target distribution (dynamic). More details
 
BIASFACTOR
The bias factor used for the well-tempered distribution
=30

# 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
=cv
 
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
=300
 
GRID_BINS
the number of bins used for the grid
=1000
 
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
=b1
... VES_LINEAR_EXPANSION

# Optimization algorithm

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 potential
OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. More details
 ...
  
BIAS
the label of the VES bias to be optimized
=b1
  
STRIDE
the frequency of updating the coefficients given in the number of MD steps
=50000
  
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
=0.25
  
FES_OUTPUT
how often the FES(s) should be written out to file
=10
  
BIAS_OUTPUT
how often the bias(es) should be written out to file
=1000
  
COEFFS_OUTPUT
 how often the coefficients should be written to file
=1
  
TARGETDIST_STRIDE
stride for updating a target distribution that is iteratively updated during the optimization
=5
... 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
=10000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,cv,b1.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