Project ID: plumID:21.044
Source: plumed.dat
Originally used with PLUMED version: 2.5.1
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# 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 AT=2.,2.,2.

# Define ion groups
gna: GROUP ATOMS=4501-4870
gcl: GROUP ATOMS=4871-5240

# Calculate the CN distribution
cn0:  COORDINATIONNUMBER SPECIESA=gna SPECIESB=gcl SWITCH={RATIONAL R_0=0.38 D_MAX=1.0} 
cn1:  COORDINATIONNUMBER SPECIESA=gcl SPECIESB=gna SWITCH={RATIONAL R_0=0.38 D_MAX=1.0}

# Select those ions within the sphere with CN>5
sphere0: INSPHERE ATOM=p DATA=cn0 RADIUS={TANH R_0=1.5}  MORE_THAN={RATIONAL R_0=5.0}
sphere1: INSPHERE ATOM=p DATA=cn1 RADIUS={TANH R_0=1.5}  MORE_THAN={RATIONAL R_0=5.0}

# A single variable for Na and Cl
COMBINE  LABEL=ncryst ARG=sphere0.morethan,sphere1.morethan POWERS=1,1 PERIODIC=NO
COMBINE  LABEL=vcryst ARG=ncryst POWERS=0.333 PERIODIC=NO

# Metadynamics
metad: METAD ARG=vcryst SIGMA=0.01 TEMP=298 PACE=1000 BIASFACTOR=200.0 HEIGHT=2.5 GRID_MIN=-1. GRID_MAX=10.


PRINT ARG=ncryst,vcryst,metad.bias STRIDE=10 FILE=COLVAR