def test_LennardJonesPair():
# just touch a bunch of stuff to make sure the work
testsys = LennardJonesPair()
assert hasattr(testsys, 'mdtraj_topology')
assert hasattr(testsys, 'topology')
assert hasattr(testsys, 'system')
assert hasattr(testsys, 'positions')
assert hasattr(testsys, 'receptor_indices')
assert hasattr(testsys, 'ligand_indices')
def __init__(self):
# must set this here since we need it to generate the state,
# will get called again in the superclass method
self.getState_kwargs = dict(GET_STATE_KWARG_DEFAULTS)
if self.GET_STATE_KWARGS is not None:
self.getState_kwargs.update(self.GET_STATE_KWARGS)
test_sys = LennardJonesPair()
init_state = self.make_state(test_sys.system, test_sys.positions)
super().__init__(
distance=PairDistance(),
init_state=init_state,
system=test_sys.system,
topology=test_sys.topology,
)
def create_sim():
test_sys = LennardJonesPair()
integrator = omm.LangevinIntegrator(300.0*unit.kelvin,
1/unit.picosecond,
0.002*unit.picoseconds)
init_state = gen_sim_state(test_sys.positions, test_sys.system, integrator)
platform = omm.Platform.getPlatformByName('CPU')
simulation = omma.Simulation(
test_sys.topology,
test_sys.system,
integrator,
platform=platform,
)
simulation.context.setState(init_state)
return simulation
import simtk.unit as unit
from openmm_systems.test_systems import LennardJonesPair
from wepy.resampling.resamplers.resampler import NoResampler
from wepy.runners.openmm import OpenMMRunner, gen_walker_state
from wepy.walker import Walker
from wepy.sim_manager import Manager
from wepy.work_mapper.mapper import Mapper
# from wepy.work_mapper.thread import ThreadMapper
# use a ready made system for OpenMM MD simulation
with start_action(action_type="Instantiate test system"):
test_sys = LennardJonesPair()
with start_action(action_type="Gen Runner"):
integrator = omm.LangevinIntegrator(300.0*unit.kelvin,
1/unit.picosecond,
0.002*unit.picoseconds)
init_state = gen_walker_state(test_sys.positions, test_sys.system, integrator)
runner = OpenMMRunner(test_sys.system, test_sys.topology, integrator,
platform='Reference')
# a trivial resampler which does nothing
with start_action(action_type="Instantiate Resampler"):
resampler = NoResampler()
def lj_omm_sys():
return LennardJonesPair()