#
protocol.massSetup()
# IVM setup
# the IVM is used for performing dynamics and minimization in torsion-angle
# space, and in Cartesian space.
#
from ivm import IVM
dyn = IVM()
# reset ivm topology for torsion-angle dynamics
#
dyn.reset()
#don't yet have proper top/par values for ACD
dyn.group("segid B")
protocol.torsionTopology(dyn)
# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)
minc.group("segid B")
protocol.cartesianTopology(minc)
# object which performs simulated annealing
#
from simulationTools import AnnealIVM
init_t = 3000. # Need high temp and slow annealing to converge
cool = AnnealIVM(initTemp=init_t,
