Normal modes of a protein using a simplified force field — MMTK User Guide 2.7.7 documentation

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# Normal modes of a protein using a simplified force field

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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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