def _get_integrator(self, thermostat):
assert thermostat in [None, "Nose", "Langevin"
], "Wrong thermostat: " + str(thermostat)
if thermostat is None:
return VelocityVerletIntegrator(self._universe, delta_t=self._dt)
elif thermostat == "Nose":
self._universe.thermostat = NoseThermostat(self._temperature)
return VelocityVerletIntegrator(self._universe, delta_t=self._dt)
elif thermostat == "Langevin":
return self._get_Langevin_integrator()
def _get_integrators(self, thermostat):
if thermostat is None:
return [
VelocityVerletIntegrator(universe, delta_t=self._time_step)
for universe in self._universes
]
elif thermostat == "Nose":
for universe in self._universes:
universe.thermostat = NoseThermostat(self._temperature)
return [
VelocityVerletIntegrator(universe, delta_t=self._time_step)
for universe in self._universes
]
elif thermostat == "Langevin":
return [
self._get_Langevin_integrator(universe)
for universe in self._universes
]
else:
raise Exception("Unknown thermostat " + thermostat)
print("Solvent molecules have been added, now shrinking universe...")
# Shrink the universe back to its original size, thereby compressing
# the solvent to its real density.
MMTK.Solvation.shrinkUniverse(universe, temperature, 'solvation.nc')
print("Universe has been compressed, now equilibrating...")
# Set a better force field and add thermostat and barostat.
#
# Note: For efficiency, optimized Ewald parameters should be used
# in a real application. The barostat relaxation time must be
# adjusted to the system size; it should be chosen smaller than
# for a realistic simulation in order to reach the final
# volume faster.
universe.setForceField(Amber94ForceField(1.4, {'method': 'ewald'}))
universe.thermostat = NoseThermostat(temperature)
universe.barostat = AndersenBarostat(pressure, 0.1*Units.ps)
# Create an integrator and a trajectory.
integrator = VelocityVerletIntegrator(universe, delta_t=1.*Units.fs)
trajectory = Trajectory(universe, "equilibration.nc", "w",
"Equilibration (NPT ensemble)")
# Start an NPT integration with periodic rescaling of velocities
# and resetting of the barostat. The number of steps required to
# reach a stable volume depends strongly on the system!
output_actions = [TrajectoryOutput(trajectory,
('configuration', 'energy', 'thermodynamic',
'time', 'auxiliary'), 0, None, 100),
LogOutput("equilibration.log", ('time', 'energy'),