nanover.openmm.simulation module

class nanover.openmm.simulation.OpenMMSimulation(name: str | None = None)

Bases: object

A wrapper for OpenMM simulations to run inside the OmniRunner.

The following attributes can be configured after construction: - frame_interval: Number of simulation steps to advance between frames. - include_velocities: Include particle velocities in frames. - include_forces: Include particle forces in frames. - platform_name: Name of OpenMM platform to use when loading the system from XML.

advance_by_one_step()

Advance the simulation to the next point a frame should be reported, and send that frame.

advance_by_seconds(dt: float)

Advance playback time by some seconds, and advance the simulation to the next frame output.

Parameters:

dt – Time to advance playback by in seconds (ignored)

advance_to_next_report()

Step the simulation to the next point a frame should be reported, and send that frame.

determine_pbcs()

Determine whether the simulation uses periodic boundary conditions and if it does, retrieve the periodic box vectors in nanometers.

frame_interval

Number of simulation steps to advance between frames.

classmethod from_simulation(simulation: Simulation, *, name: str | None = None)

Construct this from an existing OpenMM simulation.

Parameters:

• simulation – An existing OpenMM Simulation

• name – An optional name for the simulation instead of default

classmethod from_xml_path(path: PathLike[str], *, name: str | None = None)

Construct this from an existing NanoVer OpenMM XML file at a given path.

Parameters:

• path – Path of the NanoVer OpenMM XML file

• name – An optional name for the simulation instead of filename

include_forces

Include particle forces in frames.

include_velocities

Include particle velocities in frames.

load()

Load and set up the simulation if it isn’t done already.

make_regular_frame(positions: ndarray | None = None)

Make a NanoVer FrameData corresponding to the current state of the simulation.

Parameters:

positions – Optionally provided particle positions to save fetching them again.

make_topology_frame()

Make a NanoVer FrameData corresponding to the current particle positions and topology of the simulation.

pbc_vectors: ndarray | None

Array of vectors defining the periodic box used by the simulation (if PBCs are employed).

platform_name: str | None

Name of OpenMM platform to use at the time the system is loaded from XML.

reset(app_server: AppServer)

Reset the simulation to its initial conditions, reset IMD interactions, and reset frame stream to begin with topology and continue.

Parameters:

app_server – The app server hosting the frame publisher and imd state

use_pbc_wrapping: bool | None

Provide atom positions wrapped according to PBC such that each molecule has a center of mass within the primary periodic box.