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# Normal mode calculation using a simplified harmonic force field.
# For a description of the force field, see
#
# K. Hinsen & G.R. Kneller
# A simplified force field for describing vibrational protein dynamics
# over the whole frequency range
# J. Chem. Phys. 111, 10766 (1999)
#
from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import HarmonicForceField
from MMTK.NormalModes import VibrationalModes
from MMTK.Visualization import view
# Construct system
universe = InfiniteUniverse(HarmonicForceField())
universe.protein = Protein('bala1')
# 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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