polymerist.mdtools.openmmtools.preparation

Boilerplate for setting up OpenMM Simulations and related files

Attributes

LOGGER

Functions

simulation_from_thermo(→ openmm.app.Simulation)	Prepare an OpenMM simulation from a serialized thermodynamics parameter set
initialize_simulation_and_files(...)	Create simulation, bind Reporters, and update simulation Paths with newly-generated files

Module Contents

polymerist.mdtools.openmmtools.preparation.LOGGER

polymerist.mdtools.openmmtools.preparation.simulation_from_thermo(topology: openmm.app.Topology, system: openmm.System, thermo_params: polymerist.mdtools.openmmtools.thermo.ThermoParameters, time_step: openmm.unit.Quantity, positions: openmm.unit.Quantity | None = None, state: polymerist.mdtools.openmmtools.serialization.state.StateLike | None = None) → openmm.app.Simulation

Prepare an OpenMM simulation from a serialized thermodynamics parameter set

polymerist.mdtools.openmmtools.preparation.initialize_simulation_and_files(out_dir: pathlib.Path, prefix: str, sim_params: polymerist.mdtools.openmmtools.parameters.SimulationParameters, topology: openmm.app.Topology, system: openmm.System, positions: openmm.unit.Quantity | None = None, state: polymerist.mdtools.openmmtools.serialization.state.StateLike | None = None) → tuple[openmm.app.Simulation, polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths]

Create simulation, bind Reporters, and update simulation Paths with newly-generated files