from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber94ForceField
from MMTK.Minimization import SteepestDescentMinimizer
from MMTK.Minimization import ConjugateGradientMinimizer
from MMTK.Trajectory import TrajectoryOutput, StandardLogOutput
from MMTK.Visualization import view

#universeの設定
universe = InfiniteUniverse(Amber94ForceField())

#分子の読み込み
universe.protein = Protein('bala1')

#EM1
print "SteepestDescent"                                                    
minimizer1 = SteepestDescentMinimizer(universe, actions = [StandardLogOutput(50)])                 
minimizer1(steps = 200)

#EM2
print "\nConjugateGradient"
minimizer2 = ConjugateGradientMinimizer(universe, actions = [StandardLogOutput(50)])
minimizer2(steps = 100)

#表示
view(universe)