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
tested onv2.9
tested onmaster
tested on master
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details.
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=TD_TS-target-plumed2.6.cpp
UNITS
This command sets the internal units for the code. More details
NATURAL
use natural units
p:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=1 ene:
ENERGY
Calculate the total potential energy of the simulation box. More details
bf1:
BF_LEGENDRE
Legendre polynomials basis functions. More details
MINIMUM
The minimum of the interval on which the basis functions are defined
=-3
MAXIMUM
The maximum of the interval on which the basis functions are defined
=+3
ORDER
The order of the basis function expansion
=14
SCALED
Scale the polynomials such that they are orthonormal to 1

TD_TS_TARGET
This 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_EXPANSION
Linear basis set expansion bias. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=p.x
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bf1
LABEL
a label for the action so that its output can be referenced in the input to other actions
=b1
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=1.0
GRID_BINS
the number of bins used for the grid
=300
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td ... VES_LINEAR_EXPANSION
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
=500
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
=1
FES_OUTPUT
how often the FES(s) should be written out to file
=100
COEFFS_OUTPUT
how often the coefficients should be written to file
=100
TARGETDIST_OUTPUT
how often the dynamic target distribution(s) should be written out to file
=500
TARGETDIST_STRIDE
stride 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
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
=100
FILE
the name of the file on which to output these quantities
=colvar.data
FMT
the format that should be used to output real numbers
=%8.4f