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HOST: GROUP ATOMS=33-228 #host atoms
LIGC: GROUP ATOMS=1-6,8-10 #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
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