Project ID: plumID:21.012
Source: y245g/plumed.dat
Originally used with PLUMED version: 2.7
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

#vim:ft=plumed

RESTART

# COLVAR
lig: COM ATOMS=5519-5563 # you need the COM of your ligand/molecule
pbd1: COM ATOMS=3261-3284 # describe product binding domain (res 213)
pbd2: COM ATOMS=3736-3742 # describe prroduct binding domain (res 245)

# FUNNEL
wd: DISTANCE ATOMS=3616,lig # anchor dist for walls 
fps: FUNNEL_PS REFERENCE=ref.pdb LIGAND=lig ANCHOR=3616 POINTS=5.1375,4.3952,5.3672,6.5414,3.6569,5.4359

d1: DISTANCE ATOMS=pbd1,lig # For the meta, not Funnel related
d2: DISTANCE ATOMS=pbd2,lig

FUNNEL ARG=fps.lp,fps.ld ZCC=2.5 ALPHA=0.55 RCYL=0.1 MINS=-1 MAXS=6 KAPPA=50000 NBINS=500 NBINZ=500 SAFETY=1.0 SLOPE=1.0 LABEL=funnel FILE=BIAS

### METADYNAMICS ### 
METAD ...
    ARG=d1,fps.lp
    SIGMA=0.05,0.05
    HEIGHT=2.5 #kj/mol
    PACE=1000
    BIASFACTOR=8
    TEMP=300
    GRID_MIN=-0.5,-0.5
    GRID_MAX=5.0,5.0
    LABEL=metad # Not Funnel related
    WALKERS_MPI
... METAD

### WALLS ###
UPPER_WALLS ARG=fps.lp AT=4.0 KAPPA=500000.0 EXP=2 OFFSET=0 LABEL=uwall1
UPPER_WALLS ARG=fps.ld AT=1.0 KAPPA=500000.0 EXP=2 OFFSET=0 LABEL=uwall2

LOWER_WALLS ARG=fps.lp AT=0.0 KAPPA=500000.0 EXP=3 OFFSET=0 LABEL=lwall1
LOWER_WALLS ARG=fps.ld AT=0.0 KAPPA=500000.0 EXP=3 OFFSET=0 LABEL=lwall2

PRINT STRIDE=1000 ARG=* FILE=COLVAR