openpathsampling.engines.openmm.engine.OpenMMEngine

class openpathsampling.engines.openmm.engine.OpenMMEngine(topology, system, integrator, openmm_properties=None, options=None)

OpenMM dynamics engine based on OpenMM system and integrator.

The engine will create a openmm.app.Simulation instance and uses this to generate new frames.

__init__(topology, system, integrator, openmm_properties=None, options=None)

Parameters:

• topology (openpathsampling.engines.topology.MDTrajTopology) – a template snapshots which provides the topology object to be used to create the openmm engine

• system (openmm.app.System) – the openmm system object

• integrator (openmm.Integrator) – the openmm integrator object

• openmm_properties (dict) – optional setting for creating the openmm simuation object. Typical keys include GPU floating point precision. Note that by default the engine selects the fastest currently available OpenMM platform. If you want to specify the platform you will have to call engine.initialize(platform) after creating the engine.

• options (dict) –

  a dictionary that provides additional settings for the OPS engine. Allowed are

  ’n_steps_per_frame’int, default: 10

  the number of integration steps per returned snapshot

  ’n_frames_max’int, default: 5000,

  the maximal number of frames allowed for a returned trajectory object

Notes

The n_frames_max does not limit Trajectory objects in length. It only limits the maximal length of returned trajectory objects when this engine is used.

Methods

__init__(topology, system, integrator[, ...])	param topology: a template snapshots which provides the topology object to be used
apply_constraints([snapshot, position_tol, ...])	Apply position and velocity constraints to a given snapshot.
args()	Return a list of args of the __init__ function of a class
available_platforms()
base()	Return the most parent class actually derived from StorableObject
check_snapshot_type(snapshot)
count_weaks()	Return number of objects subclassed from StorableObject still in memory
descendants()	Return a list of all subclassed objects
fix_name()	Set the objects name to be immutable.
from_dict(dct)	Reconstruct an object from a dictionary representaiton
from_new_options([integrator, ...])	Create a new engine from existing, but different options or integrator
generate(snapshot[, running, direction])	Generate a trajectory consisting of ntau segments of tau_steps in between storage of Snapshots.
generate_n_frames([n_frames])	Generates n_frames, from but not including the current snapshot.
generate_next_frame()
get_uuid()
has_constraints()
idx(store)	Return the index which is used for the object in the given store.
initialize([platform])	Create the final OpenMMEngine
is_valid_snapshot(snapshot)	Test the snapshot to be valid.
iter_generate(initial[, running, direction, ...])	Return a generator that will generate a trajectory, returning the current trajectory in given intervals
minimize()
n_degrees_of_freedom()
named(name)	Name an unnamed object.
objects()	Returns a dictionary of all storable objects
reset()	Remove the simulation object and allow recreation.
reverse_uuid()
ruuid(uid)
set_as_default()
set_observer(active)	(De-)Activate observing creation of storable objects
start([snapshot])
stop(trajectory)	Nothing special needs to be done for direct-control simulations when you hit a stop condition.
stop_conditions(trajectory[, ...])	Test whether we can continue; called by generate a couple of times, so the logic is separated here.
to_dict()	Convert object into a dictionary representation
unload_context()	Unload the OpenMM context

Attributes

ACTIVE_LONG
BACKWARD
CREATION_COUNT
FORWARD
INSTANCE_UUID
base_cls	Return the base class
base_cls_name	Return the name of the base class
clear_snapshot_cache
cls	Return the class name as a string
current_snapshot
default_name	Return the default name.
default_options
dimensions
is_named	True if this object has a custom name.
mdtraj_topology
name	Return the current name of the object.
observe_objects
platform	Return the name of the currently used platform
simulation
snapshot_timestep
units