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from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber99ForceField
from VelocityVerlet import VelocityVerletIntegrator
from MMTK.Dynamics import Heater, TranslationRemover, RotationRemover
from MMTK.Trajectory import Trajectory, TrajectoryOutput, \
RestartTrajectoryOutput, StandardLogOutput
import time
# Define system
universe = InfiniteUniverse(Amber99ForceField(mod_files=['frcmod.ff99SB']))
universe.protein = Protein('bala1')
# Initialize velocities
universe.initializeVelocitiesToTemperature(50.*Units.K)
print 'Temperature: ', universe.temperature()
print 'Momentum: ', universe.momentum()
print 'Angular momentum: ', universe.angularMomentum()
# Create integrator
integrator = VelocityVerletIntegrator(universe, delta_t=1.*Units.fs)
# Heating and equilibration
integrator(steps=1000,
# Heat from 50 K to 300 K applying a temperature
# change of 0.5 K/fs; scale velocities at every step.
actions=[Heater(50.*Units.K, 300.*Units.K, 0.5*Units.K/Units.fs,
0, None, 1),
# 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 100 steps.
StandardLogOutput(100)])
# "Production" run
trajectory = Trajectory(universe, "bala1.nc", "w", "A simple test case")
integrator(steps=100,
# Remove global translation every 50 steps.
actions = [TranslationRemover(0, None, 50),
# Remove global rotation every 50 steps.
RotationRemover(0, None, 50),
# Write every second step to the trajectory file.
TrajectoryOutput(trajectory, ("time", "energy",
"configuration"),
0, None, 2),
# Write restart data every fifth step.
RestartTrajectoryOutput("restart.nc", 5),
# Log output to screen every 10 steps.
StandardLogOutput(10)])
trajectory.close()
print "Starting background thread..."
thread = integrator(steps = 10000, background = True,
actions = [TranslationRemover(0, None, 50),
RotationRemover(0, None, 50)])
print "Monitoring progress:"
while thread.is_alive():
state = thread.copyState()
if state is not None:
print "CPU time:", time.clock()
print "Simulation time:", state['time']
print "Potential energy:", state['potential_energy']
time.sleep(0.1)
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