dyn = IVM()
# Minimize in Cartesian space with only the covalent constraints.
# Note that bonds, angles and many impropers can't change with the
# internal torsion-angle dynamics
# breaks bonds topologically - doesn't change force field
dyn.potList().add(XplorPot("BOND"))
dyn.potList().add(XplorPot("ANGL"))
dyn.potList().add(XplorPot("IMPR"))
dyn.breakAllBondsIn("all")
protocol.initMinimize(dyn, numSteps=1000)
dyn.run()
#
# reset ivm topology for torsion-angle dynamics
#
dyn.reset()
dyn.potList().removeAll()
protocol.torsionTopology(dyn)
#
# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)
IVM_groupRigidSidechain(minc)
dyn = IVM()
# Minimize in Cartesian space with only the covalent constraints.
# Note that bonds, angles and many impropers can't change with the
# internal torsion-angle dynamics
# breaks bonds topologically - doesn't change force field
dyn.potList().add( XplorPot("BOND") )
dyn.potList().add( XplorPot("ANGL") )
dyn.potList().add( XplorPot("IMPR") )
dyn.breakAllBondsIn("all")
protocol.initMinimize(dyn,numSteps=1000)
dyn.run()
#
# reset ivm topology for torsion-angle dynamics
#
dyn.reset()
dyn.potList().removeAll()
protocol.torsionTopology(dyn)
#
# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)
IVM_groupRigidSidechain(minc)
