# # IVM setup # 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 #
# # IVM setup # 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 #