Exemple #1
0
#
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,