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# This example shows how to calculate Brownian modes
# for big proteins. For a description of the techniques, see
#
# K. Hinsen, A.J. Petrescu, S. Dellerue, M.C. Bellissent-Funel, G.R. Kneller
# Harmonicity in slow protein dynamics
# Chem. Phys. 261, 25 (2000)
#
from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import CalphaForceField
from MMTK.ProteinFriction import calphaFrictionConstants
from MMTK.NormalModes import BrownianModes
# Construct system
universe = InfiniteUniverse(CalphaForceField(2.5))
universe.protein = Protein('insulin.pdb', model='calpha')
# Calculate Brownian modes
modes = BrownianModes(universe, calphaFrictionConstants(universe.protein),
300.*Units.K)
# Print relaxation times for the slowest ten modes
#
# Note: realistic time scales can be expected only if the potential
# has been scaled by a protein-specific factor such that the fluctuation
# amplitudes are approximated well. That factor must in practice be
# obtained from experiment. See the publication cited above for details.
#
for i in range(6, 16):
print i, 1./modes[i].inv_relaxation_time
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