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# An example for LangevinDynamics
#
from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber94ForceField
from MMTK.Dynamics import TranslationRemover, RotationRemover, VelocityScaler
from MMTK.Trajectory import Trajectory, TrajectoryOutput, StandardLogOutput
from LangevinDynamics import LangevinIntegrator
# Define system
universe = InfiniteUniverse(Amber94ForceField())
universe.protein = Protein('bala1')
temperature = 300.*Units.K
# Initialize velocities
universe.initializeVelocitiesToTemperature(temperature)
# Set friction coefficients
friction = universe.masses()*0.01/Units.ps
# Create integrator
integrator = LangevinIntegrator(universe, delta_t=1.*Units.fs,
friction=friction, temperature=temperature)
# Equilibration
integrator(steps=10000,
actions=[# Scale velocities every 50 steps.
VelocityScaler(temperature, 0.1*temperature,
0, None, 50),
# Remove global translation every 50 steps.
TranslationRemover(0, None, 50),
# Remove global rotation every 50 steps.
RotationRemover(0, None, 50),
# Log output to screen every 500 steps.
StandardLogOutput(500)])
# "Production" run
trajectory = Trajectory(universe, "langevin.nc", "w", "Langevin test")
integrator(steps=10000,
actions = [# Remove global translation every 50 steps.
TranslationRemover(0, None, 50),
# Remove global rotation every 50 steps.
RotationRemover(0, None, 50),
# Write every fifth step to the trajectory file.
TrajectoryOutput(trajectory, ("time", "energy",
"thermodynamic",
"configuration"),
0, None, 10),
# Log output to screen every 100 steps.
StandardLogOutput(100)])
trajectory.close()
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