Project ID: plumID:21.001
Source: HS6ST/plumed.dat
Originally used with PLUMED version: 2.4
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

MOLINFO STRUCTURE=refe_sel.pdb

WHOLEMOLECULES STRIDE=10 ENTITY0=506,513,520,534,548,568,575,599,616,635,651,675,689,1737,1751,1771,1792,1813,1832,1846,1863,1882,1926,1932,1948,1959,1983,2004,2023,2034,2049,2073,2095,2112,2128,2145,3595,3615,3632,3656

# Assign atoms to group names.
# Chooses only the the water oxygens for coordination number with water (CN_W)
OW: GROUP ATOMS=5523-27022:3
S: GROUP ATOMS=5482 #paps sulfate
G: GROUP ATOMS=5460 #GlcNAc-acceptor oxygen
T: GROUP ATOMS=1248 #soluble exposed nitrogen from TRP
ene: ENERGY

dP:   DISTANCE ATOMS=S,G
cn: COORDINATION GROUPA=T GROUPB=OW R_0=0.261 NLIST NL_CUTOFF=0.6 NL_STRIDE=100

RANDOM_EXCHANGES 
INCLUDE FILE=cvs.dat
metadP: METAD ARG=dP,cn SIGMA=0.1,0.1 PACE=500 HEIGHT=1.5 BIASFACTOR=5 GRID_MIN=0,0 GRID_MAX=10,20 GRID_BIN=100,100 CALC_RCT RCT_USTRIDE=50 FILE=HILLS_dP3

LOWER_WALLS ARG=dP AT=0.0 KAPPA=35100 EXP=2 OFFSET=0 LABEL=lwall
UPPER_WALLS ARG=dP AT=1.5 KAPPA=35100 EXP=2 OFFSET=0 LABEL=uwall

PRINT ARG=uwall.bias,lwall.bias FILE=bias STRIDE=100 
PRINT ARG=dP,cn STRIDE=100  FILE=COLVAR

bias: REWEIGHT_METAD TEMP=300
HISTOGRAM ...
  ARG=dP
  GRID_MIN=0.0
  GRID_MAX=10
  GRID_BIN=100
  BANDWIDTH=0.1
  LOGWEIGHTS=bias
  LABEL=hB
... HISTOGRAM
DUMPGRID GRID=hB FILE=histoB STRIDE=100 FMT=%8.4f