Project ID: plumID:19.046
Source: PLUMED_VAC_METAD/plumed_VAC_METAD.dat
Originally used with PLUMED version: 2.5-mod
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

MOLINFO MOLTYPE=protein STRUCTURE=protein.pdb
WHOLEMOLECULES ENTITY0=1-3232

lig: COM ATOMS=3233,3236,3237,3240,3241,3243,3245,3247,3249 # you need the COM of your ligand/molecule

fps: FPS REFERENCE=Faidon_new_ref.pdb LIGAND=lig ANCHOR=2481 POINTS=-0.5910,0.3486,-1.6694,-0.6214,0.5475,-1.2516
##############################################################################################
# This is the colvar that has inside linepos and linedist (fps.lp and fps.ld, respectively).
# Starting form the obvious, POINTS are the two points A and B to construct the funnel,
# REFERENCE is a pdb file to align the target protein with the frame used to construct
# the funnel. LIGAND must have the label of the COM of the ligand. ANCHOR is one of the
# closest atoms of the protein with respect to the ligand. It's necessary to avoid pbc
# problems.
##############################################################################################

FUNNEL ARG=fps.lp,fps.ld MINS=-1.0 MAXS=3.5 NBINS=600 ZCC=1.8 ALPHA=0.55 KAPPA=35100 LABEL=funnel
##############################################################################################
# This routine creates the external BIAS of the Funnel. ARG is already set and should
# not be changed. S is the direction along linepos and MINS and MAXS define the maximum
# values that fps.lp can take. ATTENTION: if fps.lp takes a value outside this interval
# during the simulation, the simulation will crash. NBINS and NBINZ (not used here) 
# determine the binning of the external BIAS. ZCC and ALPHA regulate the shape and
# position of cone and cylinder. KAPPA is the constant used to evaluate the potential
# in each bin.
############################################################################################## 

#METAD ARG=d1 SIGMA=0.01 HEIGHT=2.0 PACE=500 BIASFACTOR=12 TEMP=300 LABEL=metad # Not Funnel related

UPPER_WALLS ARG=fps.lp AT=3.0 KAPPA=500000.0 EXP=3 OFFSET=0 LABEL=uwall
##############################################################################################
# Here pick a value lower than MAXS, the ligand MUST NOT exit the grid
##############################################################################################

LOWER_WALLS ARG=fps.lp AT=-0.3 KAPPA=500000.0 EXP=3 OFFSET=0 LABEL=lwall
##############################################################################################
# Here pick a value greater than MINS, the ligand MUST NOT exit the grid
##############################################################################################
RMSD REFERENCE=pocket.pdb TYPE=OPTIMAL LABEL=rmsd
UPPER_WALLS ARG=rmsd AT=1.2 KAPPA=500000.0 EXP=3 OFFSET=0 LABEL=rmsdwall # Not Funnel related


rmsdINIT: RMSD REFERENCE=my_start_meta.pdb TYPE=OPTIMAL
UPPER_WALLS ARG=rmsdINIT AT=0.09 KAPPA=420000 EXP=2 OFFSET=0 LABEL=rmsdwallINIT 



OW: GROUP ATOMS=3251-47362:3
c1: COM ATOMS=2473-2495,2913-2919
c2: COM ATOMS=3240
dcm: DISTANCE ATOMS=c1,c2

c3: COM ATOMS=2480
c4: COM ATOMS=3236
dsb: DISTANCE ATOMS=c3,c4

#t: TORSION ATOMS=2915,2780,3241,3247
ALPHABETA ...
ATOMS1=2915,2780,3241,3247 REFERENCE=1.66
LABEL=ab_t
... ALPHABETA

Prot:  DISTANCES GROUPA=3233,3236,3237,3240,3241,3243,3245,3247,3249 GROUPB=1-3232 LESS_THAN={RATIONAL R_0=0.32 NN=6 MM=12}
COMBINE ARG=Prot.lessthan COEFFICIENTS=0.012 POWERS=1 LABEL=Prot_norm PERIODIC=NO
COMBINE ARG=dsb COEFFICIENTS=0.3125 POWERS=1 LABEL=dsb_norm PERIODIC=NO


#####


BRIDGE BRIDGING_ATOMS=OW GROUPA=2805 GROUPB=2489 SWITCH={RATIONAL R_0=0.6 D_0=0.0 NN=6 MM=10 D_MAX=4.0} LABEL=wBpock
COMBINE ARG=wBpock COEFFICIENTS=0.1538 POWERS=1 LABEL=wBpock_norm PERIODIC=NO


####

lig_OW_large: DISTANCES GROUPA=3233,3236,3237,3240,3241,3243,3245,3247,3249 GROUPB=OW  LESS_THAN={RATIONAL R_0=0.8 NN=6 MM=12 D_MAX=0.4}
COMBINE ARG=lig_OW_large.lessthan COEFFICIENTS=0.01551 POWERS=1 LABEL=lig_OW_large_norm PERIODIC=NO

COMBINE ARG=Prot_norm,wBpock_norm,ab_t,lig_OW_large_norm COEFFICIENTS=-3.874476e-01,7.813634e-01,-1.941195e-01,4.490805e-01 LABEL=tica1_vasi3_with_tor_norm_Prot_solv PERIODIC=NO
COMBINE ARG=Prot_norm,wBpock_norm,ab_t,lig_OW_large_norm COEFFICIENTS=1.102318e-02,-8.507166e-01,-2.917756e-01,4.370660e-01 LABEL=tica2_vasi3_with_tor_norm_Prot_solv PERIODIC=NO



METAD ...
 LABEL=metad
 ARG=tica1_vasi3_with_tor_norm_Prot_solv,tica2_vasi3_with_tor_norm_Prot_solv   
 SIGMA=0.045,0.055
 HEIGHT=2.5  
 BIASFACTOR=15 
 TEMP=300 
 PACE=250
 GRID_MIN=-4,-4 
 GRID_MAX=4,4
 GRID_BIN=600,500
 REWEIGHTING_NGRID=600,500
 REWEIGHTING_NHILLS=20
... METAD

rw: REWEIGHT_METAD TEMP=300

PRINT ARG=* FILE=COLVAR STRIDE=250

#PRINT ARG=dsb,t,dcm,w.lessthan,rmsd,metad.* FILE=COLVAR STRIDE=250