Project ID: plumID:21.044
Source: plumed.dat
Originally used with PLUMED version: 2.5.1
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 onv2.8
tested onmaster
# From NaCl Crystallisation Pathways; Aaron R. Finney and Matteo Salvalaglio
# Plumed input file to run metadynamics to bias the size of NaCl clusters around a point in the centre of solution

# Fix an atom at the centre of the simulation box p:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.,2.,2
# Define ion groups gna:
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
=4501-4870 gcl:
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
=4871-5240
# Calculate the CN distribution cn0:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=gna
SPECIESB
this keyword is used for colvars such as the coordination number
=gcl
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0} cn1:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=gcl
SPECIESB
this keyword is used for colvars such as the coordination number
=gna
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
# Select those ions within the sphere with CN>5 sphere0:
INSPHERE
This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details
ATOM
the atom whose vicinity we are interested in examining
=p
DATA
The multicolvar that calculates the set of base quantities that we are interested in
=cn0
RADIUS
the switching function that tells us the extent of the spherical region of interest
={TANH R_0=1.5}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0} sphere1:
INSPHERE
This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details
ATOM
the atom whose vicinity we are interested in examining
=p
DATA
The multicolvar that calculates the set of base quantities that we are interested in
=cn1
RADIUS
the switching function that tells us the extent of the spherical region of interest
={TANH R_0=1.5}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0}
# A single variable for Na and Cl
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
=ncryst
ARG
the input for this action is the scalar output from one or more other actions
=sphere0.morethan,sphere1.morethan
POWERS
the powers to which you are raising each of the arguments in your function
=1,1
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
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
=vcryst
ARG
the input for this action is the scalar output from one or more other actions
=ncryst
POWERS
the powers to which you are raising each of the arguments in your function
=0.333
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# Metadynamics metad:
METAD
Used to performed metadynamics on one or more collective variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=vcryst
SIGMA
the widths of the Gaussian hills
=0.01
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298
PACE
the frequency for hill addition
=1000
BIASFACTOR
use well tempered metadynamics and use this bias factor
=200.0
HEIGHT
the heights of the Gaussian hills
=2.5
GRID_MIN
the lower bounds for the grid
=-1
GRID_MAX
the upper bounds for the grid
=10
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=ncryst,vcryst,metad.bias
STRIDE
the frequency with which the quantities of interest should be output
=10
FILE
the name of the file on which to output these quantities
=COLVAR