Project ID: plumID:19.080
Source: ohco2/symm-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
tested onv2.9
tested onmaster
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
=2,3
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1
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
=d2
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=3
R_0
The r_0 parameter of the switching function
=1.75
NN
The n parameter of the switching function
=4
LABEL
a label for the action so that its output can be referenced in the input to other actions
=coord
ANGLE
Calculate an angle. More details
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=4,3,5
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ang
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=3
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=4
R_0
The r_0 parameter of the switching function
=1.15
NN
The n parameter of the switching function
=12
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dis1
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=3
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5
R_0
The r_0 parameter of the switching function
=1.15
NN
The n parameter of the switching function
=12
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dis2
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=dis1,dis2
COEFFICIENTS
the coefficients of the arguments in your function
=0.5,0.5
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
=nm
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
AT
the positions of the wall
=2.5
KAPPA
the force constant for the wall
=100.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=constrain1
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
=d2
AT
the positions of the wall
=1.3
KAPPA
the force constant for the wall
=500.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=constrain2
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
=nm
FILE
the name of the file containing the external potential
=extbias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=external
bf1:
BF_CHEBYSHEV
Chebyshev polynomial basis functions. More details
MINIMUM
The minimum of the interval on which the basis functions are defined
=1
MAXIMUM
The maximum of the interval on which the basis functions are defined
=3.0
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
=d1
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
=400
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
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
=4000
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
=10
BIAS_OUTPUT
how often the bias(es) should be written out to file
=1000
FES_PROJ_OUTPUT
how often the projections of the FES(s) should be written out to file
=10
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
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
=200
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,coord,ang,b1.bias
STRIDE
the frequency with which the quantities of interest should be output
=200
FILE
the name of the file on which to output these quantities
=colvar