Project ID: plumID:21.038
Source: UreaNucleationFromMelt/chi4.dat
Originally used with PLUMED version: 2.6.1
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
tested on master
# Restart simulation. This command will append results of new simulations to the same output files, e.g. COLVAR.

LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=PairOrientationalEntropy.cpp
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=ManyAngle2_ST.cpp
# Define groups for the CV
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
FILE
file to be included
=centers.dat
C:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=1-864:8 O:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=2-864:8 N1:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=3-864:8 N2:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=6-864:8 # Define the CV
PAIR_ORIENTATIONAL_ENTROPY
This action is not part of PLUMED and was included by using a LOAD command More details
... LABEL=s1 CENTER=C START=Ncenter END=O MAXR=0.6 SIGMA=0.05,0.25 ... PAIR_ORIENTATIONAL_ENTROPY
PAIR_ORIENTATIONAL_ENTROPY
This action is not part of PLUMED and was included by using a LOAD command More details
... LABEL=s2 CENTER=C START=N1 END=N2 MAXR=0.6 SIGMA=0.05,0.125 UP_DOWN_SYMMETRY ... PAIR_ORIENTATIONAL_ENTROPY
MANY_ANGLE
This action is not part of PLUMED and was included by using a LOAD command More details
... LABEL=ma1 CENTER=C START=C END=O RCUT=0.64 NOPBC ... MANY_ANGLE
MANY_ANGLE
This action is not part of PLUMED and was included by using a LOAD command More details
... LABEL=ma2 CENTER=C START=N1 END=N2 RCUT=0.64 NOPBC ... MANY_ANGLE
# Construct a bias potential using metadynamics
COMBINE
Calculate a polynomial combination of a set of other variables. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rc
ARG
the input to this function
=s1,s2,ma1,ma2
COEFFICIENTS
the coefficients of the arguments in your function
=0.513,0.938,-0.129,1.00
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... COMBINE
METAD
Used to performed metadynamics on one or more collective variables. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
ARG
the input for this action is the scalar output from one or more other actions
=rc # Label of the CV
PACE
the frequency for hill addition
=2500 # Pace in the deposition of the gaussians
HEIGHT
the heights of the Gaussian hills
=18.705 # Height of the gaussians in energy units kJ/mol. This is 5 kT.
SIGMA
the widths of the Gaussian hills
=0.10 # Width of the gaussian in CV units
FILE
a file in which the list of added hills is stored
=HILLS # File where the information of the gaussians is printed
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50.0 # Bias factor in well tempered simulations
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=450.0 # Temperature in Kelvin. Only needed for well tempered simulations
GRID_MIN
the lower bounds for the grid
=-20.0 # The following three lines define a grid for the calculation of the bias potential. Use it **always**.
GRID_MAX
the upper bounds for the grid
=2.0
GRID_BIN
the number of bins for the grid
=600
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
# Print value of the CV and bias to a file named COLVAR
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=500
ARG
the input for this action is the scalar output from one or more other actions
FILE
the name of the file on which to output these quantities
=COLVAR