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# A normal mode calculation in the subspace of a part of the total system.
#
from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber94ForceField
from MMTK.NormalModes import VibrationalModes
from MMTK.Subspace import Subspace
from MMTK.Minimization import ConjugateGradientMinimizer
from MMTK.Trajectory import StandardLogOutput
from Scientific import N
# Construct system
universe = InfiniteUniverse(Amber94ForceField())
universe.protein1 = Protein('bala1')
universe.protein2 = Protein('bala1')
universe.protein2.translateBy(Vector(1., 0., 0.))
# Define normal mode subspace
class SubsetSubspace(Subspace):
def __init__(self, universe, objects):
vectors = []
for a in objects.atomList():
for d in [Vector(1.,0.,0.), Vector(0.,1.,0.), Vector(0.,0.,1.)]:
v = ParticleProperties.ParticleVector(universe)
v[a] = d
vectors.append(v)
Subspace.__init__(self, universe, vectors)
subspace = SubsetSubspace(universe, universe.protein1)
# Minimize
minimizer = ConjugateGradientMinimizer(universe,
actions=[StandardLogOutput(50)])
minimizer(convergence = 1.e-3, steps = 10000)
# Calculate normal modes
modes = VibrationalModes(universe, subspace=subspace)
# Print frequencies
for mode in modes:
print mode
# Show animation of the first mode
modes[0].view()
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