PLUMED-NEST

Project ID: plumID:19.014
Source: mil-101_paper_setup/plumed_files/plumed_coordination.dat
Originally used with PLUMED version: 2.2
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

RESTART
Activate restart. More details

The RESTART action with label  calculates something
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cnThe COORDINATIONNUMBER action with label cn calculates the following quantities:
 Quantity   
 Type   
 Description  
cn
vector
the value calculated by this action
cn_morethan
scalar
the number of colvars that have a value more than a threshold 
SPECIESA
this keyword is used for colvars such as the coordination number
=1-3,61-63 
SPECIESB
this keyword is used for colvars such as the coordination number
=23,24,39,40,55,56,83,84,99,100,115,116 
R_0
The r_0 parameter of the switching function
=0.25 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn 
SPECIESA
this keyword is used for colvars such as the coordination number
=1-3,61-63 
SPECIESB
this keyword is used for colvars such as the coordination number
=23,24,39,40,55,56,83,84,99,100,115,116 
R_0
The r_0 parameter of the switching function
=0.25 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}  
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=0
# PLUMED interprets the command:
# COORDINATIONNUMBER LABEL=cn SPECIESA=1-3,61-63 SPECIESB=23,24,39,40,55,56,83,84,99,100,115,116 R_0=0.25 MORE_THAN={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
# as follows (Click the red comment above to revert to the short version of the input):
cn_grpThe GROUP action with label cn_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_grp
atoms
indices of atoms specified in GROUP: 
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
=1-3,61-63 
cn_matThe CONTACT_MATRIX action with label cn_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
R_0
The r_0 parameter of the switching function
=0.25 
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=0 
cn_onesThe CONSTANT action with label cn_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=12
cnThe MATRIX_VECTOR_PRODUCT action with label cn calculates the following quantities:
 Quantity   
 Type   
 Description  
cn
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cn_mat,cn_ones 
cn_caverageThe MEAN action with label cn_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_caverage
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cn 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
cn_mtThe MORE_THAN action with label cn_mt calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_mt
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the input to this function
=cn 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0} 
cn_morethanThe SUM action with label cn_morethan calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_morethan
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=cn_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
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
=cn.morethan 
SIGMA
the widths of the Gaussian hills
=0.01 
HEIGHT
the heights of the Gaussian hills
=2.5 
PACE
the frequency for hill addition
=500
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50 
FILE
 a file in which the list of added hills is stored
=hills
GRID_MIN
the lower bounds for the grid
=-0.5 
GRID_MAX
the upper bounds for the grid
=6 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.002 
GRID_SPARSE
 use a sparse grid to store hills
... METAD

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
ARG
the input for this action is the scalar output from one or more other actions
=cn.morethan,metad.bias 
FILE
the name of the file on which to output these quantities
=colvar

ENDPLUMED
Terminate plumed input. More details