def create_sim_openmm(model, anchor, output_filename, state_prefix=None):
"""
Take all relevant model and anchor information and generate
the necessary OpenMM objects to run the simulation.
Parameters
----------
model : Model()
The Model which contains the anchor and all settings for
the simulation that is about to be run.
anchor : Anchor()
The anchor object that this OpenMM simulation applies to.
output_filename : str
The name of the directory that will be written by the plugin as
the Elber simulation proceeds, recording every 'bounce'.
state_prefix : str or None
The plugin can optionally save every state during a
bounce. These can be used to seed simulations in other
cells. This argument provides the file prefix for these
saved states. If None, then no states will be written.
Returns
-------
sim_openmm : Sim_openmm()
The sim_openmm object, which contains everything needed
to run an MMVT simulation within OpenMM.
"""
sim_openmm = Elber_sim_openmm()
fwd_output_filename = output_filename
directory = os.path.dirname(output_filename)
basename = os.path.basename(output_filename)
suffix = re.sub(elber_base.OPENMM_ELBER_BASENAME, "", basename)
rev_basename = elber_base.ELBER_REV_BASENAME+suffix
rev_output_filename = os.path.join(directory, rev_basename)
sim_openmm.rev_output_filename = rev_output_filename
sim_openmm.fwd_output_filename = fwd_output_filename
sim_openmm.output_filename = output_filename
umbrella_system, umbrella_topology, umbrella_positions, \
umbrella_box_vectors, umbrella_num_frames \
= common_sim_openmm.create_openmm_system(sim_openmm, model, anchor)
rev_system, rev_topology, rev_positions, rev_box_vectors, rev_num_frames \
= common_sim_openmm.create_openmm_system(sim_openmm, model, anchor)
fwd_system, fwd_topology, fwd_positions, fwd_box_vectors, fwd_num_frames \
= common_sim_openmm.create_openmm_system(sim_openmm, model, anchor)
sim_openmm.umbrella_system = umbrella_system
sim_openmm.rev_system = rev_system
sim_openmm.fwd_system = fwd_system
add_integrators(sim_openmm, model, state_prefix=state_prefix)
common_sim_openmm.add_barostat(umbrella_system, model)
common_sim_openmm.add_barostat(rev_system, model)
common_sim_openmm.add_barostat(fwd_system, model)
common_sim_openmm.add_platform(sim_openmm, model)
add_forces(sim_openmm, model, anchor)
add_simulations(sim_openmm, model, umbrella_topology, umbrella_positions,
umbrella_box_vectors)
return sim_openmm
def create_sim_openmm(model,
anchor,
output_filename,
state_prefix=None,
frame=0,
load_state_file=None):
"""
Take all relevant model and anchor information and generate
the necessary OpenMM objects to run the simulation.
Parameters
----------
model : Model()
The Model which contains the anchor and all settings for
the simulation that is about to be run.
anchor : Anchor()
The anchor object that this OpenMM simulation applies to.
output_filename : str
The name of the file that will be written by the plugin as
the MMVT simulation proceeds, recording every 'bounce'.
state_prefix : str or None
The plugin can optionally save every state during a
bounce. These can be used to seed simulations in other
cells. This argument provides the file prefix for these
saved states. If None, then no states will be written.
frame : int
Which frame of the starting positions file to retrieve.
Returns
-------
sim_openmm : Sim_openmm()
The sim_openmm object, which contains everything needed
to run an MMVT simulation within OpenMM.
"""
sim_openmm = MMVT_sim_openmm()
sim_openmm.output_filename = output_filename
system, topology, positions, box_vectors, num_frames \
= common_sim_openmm.create_openmm_system(
sim_openmm, model, anchor, frame, load_state_file=load_state_file)
sim_openmm.system = system
add_integrator(sim_openmm, model, state_prefix=state_prefix)
common_sim_openmm.add_barostat(system, model)
common_sim_openmm.add_platform(sim_openmm, model)
add_forces(sim_openmm, model, anchor)
positions = add_simulation(sim_openmm, model, topology, positions,
box_vectors, load_state_file)
if anchor.__class__.__name__ == "MMVT_toy_anchor":
out_file_name = os.path.join(model.anchor_rootdir, anchor.directory,
anchor.building_directory, "toy.pdb")
common_sim_openmm.write_toy_pdb_file(topology, positions,
out_file_name)
return sim_openmm
def test_add_platform_ref(toy_mmvt_model):
my_sim_openmm = common_sim_openmm.Common_sim_openmm()
anchor = toy_mmvt_model.anchors[0]
system, topology, positions, box_vectors, num_frames \
= common_sim_openmm.create_openmm_system(
my_sim_openmm, toy_mmvt_model, anchor, frame=0)
common_sim_openmm.add_platform(my_sim_openmm, toy_mmvt_model)
assert my_sim_openmm.platform.getName() == "Reference"
assert my_sim_openmm.properties == {}
def test_create_openmm_system(toy_mmvt_model, host_guest_mmvt_model):
my_sim_openmm = common_sim_openmm.Common_sim_openmm()
anchor = toy_mmvt_model.anchors[0]
system, topology, positions, box_vectors, num_frames \
= common_sim_openmm.create_openmm_system(
my_sim_openmm, toy_mmvt_model, anchor, frame=0, load_state_file=None)
assert num_frames == 2
assert np.isclose(positions, np.array([[0.0, -0.7, 0.0]])\
*unit.nanometers).all()
system2, topology2, positions2, box_vectors2, num_frames2 \
= common_sim_openmm.create_openmm_system(
my_sim_openmm, toy_mmvt_model, anchor, frame=1, load_state_file=None)
assert np.isclose(positions2, np.array([[0.3, -0.7, 0.0]])\
*unit.nanometers).all()
anchor2 = host_guest_mmvt_model.anchors[0]
system3, topology3, positions3, box_vectors3, num_frames3 \
= common_sim_openmm.create_openmm_system(
my_sim_openmm, host_guest_mmvt_model, anchor2)
def test_add_platform_cuda(host_guest_mmvt_model):
host_guest_mmvt_model.openmm_settings.cuda_platform_settings\
.cuda_device_index = "2"
my_sim_openmm = common_sim_openmm.Common_sim_openmm()
anchor = host_guest_mmvt_model.anchors[0]
system, topology, positions, box_vectors, num_frames \
= common_sim_openmm.create_openmm_system(
my_sim_openmm, host_guest_mmvt_model, anchor, frame=0)
common_sim_openmm.add_platform(my_sim_openmm, host_guest_mmvt_model)
assert my_sim_openmm.platform.getName() == "CUDA"
assert my_sim_openmm.properties["CudaPrecision"] == "mixed"
assert my_sim_openmm.properties["CudaDeviceIndex"] == "2"
def test_add_barostat(host_guest_mmvt_model_npt):
my_sim_openmm = common_sim_openmm.Common_sim_openmm()
anchor = host_guest_mmvt_model_npt.anchors[0]
system, topology, positions, box_vectors, num_frames \
= common_sim_openmm.create_openmm_system(
my_sim_openmm, host_guest_mmvt_model_npt, anchor, frame=0)
forces = system.getForces()
old_force_len = len(forces)
common_sim_openmm.add_barostat(system, host_guest_mmvt_model_npt)
forces2 = system.getForces()
assert len(forces2) == old_force_len + 1
barostat = forces2[-1]
pressure = barostat.getDefaultPressure()
assert pressure == 1.0 * unit.bar
temperature = barostat.getDefaultTemperature()
assert temperature == 298.15 * unit.kelvin
def get_starting_structure_num_frames(model,
anchor,
dummy_outfile,
load_state_file=None):
"""
For an anchor's starting structure, find and return the number of frames.
"""
if load_state_file is None:
sim_openmm = MMVT_sim_openmm()
sim_openmm.output_filename = dummy_outfile
dummy_system, dummy_topology, dummy_positions, dummy_box_vectors, \
num_frames = common_sim_openmm.create_openmm_system(
sim_openmm, model, anchor)
else:
num_frames = 1
return num_frames
def create_sim_openmm(model, anchor, output_filename, state_prefix=None):
"""
Take all relevant model and anchor information and generate
the necessary OpenMM objects to run the simulation.
Parameters
----------
model : Model()
The Model which contains the anchor and all settings for
the simulation that is about to be run.
anchor : Anchor()
The anchor object that this OpenMM simulation applies to.
output_filename : str
The name of the file that will be written by the plugin as
the MMVT simulation proceeds, recording every 'bounce'.
state_prefix : str or None
The plugin can optionally save every state during a
bounce. These can be used to seed simulations in other
cells. This argument provides the file prefix for these
saved states. If None, then no states will be written.
Returns
-------
sim_openmm : Sim_openmm()
The sim_openmm object, which contains everything needed
to run an MMVT simulation within OpenMM.
"""
sim_openmm = MMVT_sim_openmm()
common_sim_openmm.fill_generic_parameters(sim_openmm, model, anchor,
output_filename)
system, topology, positions, box_vectors \
= common_sim_openmm.create_openmm_system(sim_openmm, model, anchor)
sim_openmm.system = system
add_integrator(sim_openmm, model, state_prefix=state_prefix)
common_sim_openmm.add_barostat(sim_openmm, model)
common_sim_openmm.add_platform(sim_openmm, model)
add_forces(sim_openmm, model, anchor)
add_simulation(sim_openmm, model, topology, positions, box_vectors)
return sim_openmm