PLUMED-NEST

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

# 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} 
The COORDINATIONNUMBER action with label cn0 calculates a scalar quantitycn1:  
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
The COORDINATIONNUMBER action with label cn1 calculates a scalar quantitysphere0: 
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}
The INSPHERE action with label sphere0 calculates the following quantities:
 Quantity   
 Description  
sphere0.morethan
the number of values more than a target valuesphere1: 
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
The INSPHERE action with label sphere1 calculates the following quantities:
 Quantity   
 Description  
sphere1.morethan
the number of values more than a target value
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
The COMBINE action with label ncryst calculates a scalar quantity
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
The COMBINE action with label vcryst calculates a scalar quantitymetad: 
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


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
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