PLUMED-NEST

Project ID: plumID:19.049
Source: plumed_lj_gas_liquid.dat
Originally used with PLUMED version: not specified
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

#SETTINGS NATOMS=32768
# Calculate the coordination numbers of the 100 atoms in the system
lq: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-100 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=0.45  D_MAX=0.55} 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
# Construct a contact matrix between the atoms in the system   
cm: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
ATOMS
the atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)
=lq  
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={CUBIC D_0=0.45  D_MAX=0.55} 
# Use depth first clustering to identify the sizes of the clusters                     
dfs: 
DFSCLUSTERING
Find the connected components of the matrix using the depth first search clustering algorithm. More details
 
MATRIX
the input matrix (can use ARG instead)
=cm 
# Compute the sum of the coordination numbers for the atoms in the largest cluster                                                         
The DFSCLUSTERING action with label dfs calculates a scalar quantityclust1: 
CLUSTER_PROPERTIES
Calculate properties of the distribution of some quantities that are part of a connected component More details
 
CLUSTERS
the label of the action that does the clustering
=dfs 
ARG
calculate the sum of the arguments calculated by this action for the cluster
=lq 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1 
SUM
 calculate the sum of all the quantities
  
# Apply a metadynamics bias on the sum of the coordination number for the atoms 
# in the largest cluster so as to force droplets of liquid to condense and evaporate 
mt: 
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
=clust1.sum 
SIGMA
the widths of the Gaussian hills
=10 
HEIGHT
the heights of the Gaussian hills
=2 
PACE
the frequency for hill addition
=500 
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=80.7 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50 
GRID_MIN
the lower bounds for the grid
=0 
GRID_MAX
the upper bounds for the grid
=6000
... 
# Calculate the number of atoms in the largest cluster 
The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potentialss: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest More details
 
CLUSTERS
the label of the action that does the clustering
=dfs 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1
# Output the number of atoms in the largest cluster to a file
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ss 
FILE
the name of the file on which to output these quantities
=colvar