Project ID: plumID:19.049
Source: plumed_lj_gas_liquid.dat
Originally used with PLUMED version: not specified
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# Calculate the coordination numbers of the 100 atoms in the system
lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55} LOWMEM
# Construct a contact matrix between the atoms in the system   
cm: CONTACT_MATRIX ATOMS=lq  SWITCH={CUBIC D_0=0.45  D_MAX=0.55} 
# Use depth first clustering to identify the sizes of the clusters                     
dfs: DFSCLUSTERING MATRIX=cm 
# Compute the sum of the coordination numbers for the atoms in the largest cluster                                                         
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM  
# 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 ...
 ARG=clust1.sum SIGMA=10. HEIGHT=2. PACE=500 
 TEMP=80.7 BIASFACTOR=50 GRID_MIN=0 GRID_MAX=6000
... 
# Calculate the number of atoms in the largest cluster 
ss: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=1
# Output the number of atoms in the largest cluster to a file
PRINT ARG=ss FILE=colvar