Project ID: plumID:21.038
Source: UreaNucleationFromMelt/chi6.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

ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

vol: 
VOLUME
Calculate the volume of the simulation box. More details


# 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

COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn 
SPECIES
this keyword is used for colvars such as coordination number
=Ncenter 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.6 D_MAX=0.8} 
MEAN
 calculate the mean of all the quantities


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
=enthalpy
 
ARG
the input to this function
=ene,vol
 
COEFFICIENTS
 the coefficients of the arguments in your function
=1.0,0.060221409
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

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
=h
 
ARG
the input to this function
=enthalpy
 
POWERS
 the powers to which you are raising each of the arguments in your function
=1
 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.00926
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

# 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,cn.mean,h 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.885,0.330,0.906,1.000,-0.011,-0.017 
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
=500   # Pace in the deposition of the gaussians
 
HEIGHT
the heights of the Gaussian hills
=7.482   # Height of the gaussians in energy units kJ/mol. This is 2 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
=100.0   # 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
=-5.0   # 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
=15.0
 
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
=s1,s2,ma1,ma2,cn.mean,h,metad.rbias 
FILE
the name of the file on which to output these quantities
=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
=rc,metad 
FILE
the name of the file on which to output these quantities
=METAD