# Define 3 COMs of three rigid domains
MOLINFO MOLTYPE=protein STRUCTURE=prot_md.pdb
core: COM ATOMS=148,170,189,208,228,244,260,267,1376,1396,1415,1434,1446,1771,1790,1809,1828,1849,1865,1877,2699,2715,2739,2761,2777,2791
lid: COM ATOMS=1896,1908,1923,1937,1954,1968,1990,2014,2033,2052,2074,2098,2105,2120,2134,2145,2152
nmp: COM ATOMS=781,791,815,822,844,861,880,891,906,925,942,957,979,986
hinge: COM ATOMS=2430,2451,2473,2483,2497
# setup 3 CVs for 3adk
theta1: ANGLE ATOMS=lid,hinge,core
theta2: ANGLE ATOMS=nmp,hinge,core
disln: DISTANCE ATOMS=nmp,lid
#
# Plumed units: kJ/mol, nm, ps
# Activate metadynamics in theta1,theda2,disln
# depositing a Gaussian every 500 time steps,
# with height equal to 0.1 kJoule/mol=0.1x4.184=0.42 kCal/mol,
# and width 0.05 rad for both CVs.
# Well-tempered metadynamics is activated,
# and the biasfactor is set to 6.0
# metad: METAD ARG=theta1,theta2 PACE=500 HEIGHT=0.4 SIGMA=0.05,0.05 FILE=HILLS BIASFACTOR=6.0 TEMP=300.0
#

# monitor the two variables and the metadynamics bias potential
# PRINT STRIDE=500 ARG=theta1,theta2,disln metad.bias FILE=colvar
PRINT STRIDE=500 ARG=theta1,theta2,disln FILE=colvar