| HOST: GROUP ATOMS=16-211 #host atoms | |
| LIGC: GROUP ATOMS=1-6 #carbon atoms in the ligand | |
| WHOLEMOLECULES ENTITY0=HOST | |
| FIT_TO_TEMPLATE STRIDE=1 REFERENCE=conf_template.pdb TYPE=OPTIMAL #coordinates alignment | |
| lig: CENTER ATOMS=LIGC | |
| v1: FIXEDATOM AT=2.0136,2.0136,2.0 #virtual atoms | |
| cyl: DISTANCE ATOMS=v1,lig COMPONENTS | |
| radius: MATHEVAL ARG=cyl.x,cyl.y FUNC=sqrt(x*x+y*y) PERIODIC=NO | |
| funnel: MATHEVAL ARG=radius,cyl.z VAR=r,z FUNC=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1.) PERIODIC=NO | |
| UPPER_WALLS AT=0 ARG=funnel KAPPA=2000.0 LABEL=funnelwall #funnel restraint | |
| UPPER_WALLS AT=1.8 ARG=cyl.z KAPPA=4000.0 EXP=2 LABEL=upper_wall #upper limit of cyl.z | |
| PRINT ARG=* STRIDE=250 FILE=COLVAR FMT=%8.4f | |
| ENDPLUMED | |