Project ID: plumID:21.011
Source: NaCl_at_graphite-cmumd/coordination-profiles.plmd
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 onv2.9
tested onmaster
# Define atom groups
gra: 
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
=1-9152:1 
wat: 
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
=9153-43319:3
sod: 
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
=43320-43737:1
chl: 
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
=43738-44155:1
slt: 
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
=43320-44155:1
sln: 
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
=9153-44155:1 

# Set a virtual atom at the origin and in the 'bulk'
p0: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,7.403535
p1: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,11.403535

# Get the coordination number distributions
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
=sod 
SPECIESB
this keyword is used for colvars such as the coordination number
=chl 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.355 NN=32 MM=64}
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
=sod 
SPECIESB
this keyword is used for colvars such as the coordination number
=wat 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.325 NN=32 MM=64}
cn2:  
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
=chl 
SPECIESB
this keyword is used for colvars such as the coordination number
=wat 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.385 NN=32 MM=64}
cn3:  
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
=sod 
SPECIESB
this keyword is used for colvars such as the coordination number
=gra 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.365 NN=32 MM=64}
ips: 
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=cn0 
SWITCH
the switching function that transform
={GAUSSIAN D_0=0.9999 R_0=0.00001}

densnacl: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn0 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densnaow: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn1 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densclow: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn2 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densnagra: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=cn3 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1
densips: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=ips 
ORIGIN
we will use the position of this atom as the origin
=p0 
DIR
the direction in which to calculate the density profile
=z 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=1480 
KERNEL
 the kernel function you are using
=GAUSSIAN 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
NORMALIZATION
set true/false to determine how to the data is normalised
=true 
STRIDE
 the frequency with which to accumulate the densities
=1

DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densnacl 
FILE
 the file on which to write the grid
=DENSna-cl.dat

DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densnaow 
FILE
 the file on which to write the grid
=DENSna-ow.dat

DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densclow 
FILE
 the file on which to write the grid
=DENScl-ow.dat

DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densnagra 
FILE
 the file on which to write the grid
=DENSna-gra.dat

DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=densips 
FILE
 the file on which to write the grid
=DENSips.dat