Normal modes of a proteinΒΆ

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# Standard normal mode calculation.
#

from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber94ForceField
from MMTK.NormalModes import VibrationalModes
from MMTK.Minimization import ConjugateGradientMinimizer
from MMTK.Trajectory import StandardLogOutput
from MMTK.Visualization import view

# Construct system
universe = InfiniteUniverse(Amber94ForceField())
universe.protein = Protein('bala1')

# Minimize
minimizer = ConjugateGradientMinimizer(universe,
                                       actions=[StandardLogOutput(50)])
minimizer(convergence = 1.e-3, steps = 10000)

# Calculate normal modes
modes = VibrationalModes(universe)

# Print frequencies
for mode in modes:
    print mode

# Show animation of the first non-trivial mode 
view(modes[6])

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