iphasimulator.simulation_openmm_amber_runner

OpenMM runner for AMBER topology files.

Exceptions

OpenMMRunnerError

Raised when OpenMM is unavailable or simulation setup fails.

Classes

OpenMMOutputs	Files produced by an OpenMM AMBER-topology run.
OpenMMStageTimings	Wall-clock timings for an OpenMM AMBER workflow.

Functions

openmm_available(→ bool)	Return True when OpenMM can be imported.
run_openmm_with_amber_topology(→ OpenMMOutputs)	Run minimization, NVT, NPT when periodic, and production from AMBER files.

Module Contents

class iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs

Files produced by an OpenMM AMBER-topology run.

output_dir: pathlib.Path

minimized_pdb_path: pathlib.Path

trajectory_path: pathlib.Path

state_xml_path: pathlib.Path

log_path: pathlib.Path

nvt_trajectory_path: pathlib.Path

nvt_log_path: pathlib.Path

npt_trajectory_path: pathlib.Path

npt_log_path: pathlib.Path

production_trajectory_path: pathlib.Path

production_log_path: pathlib.Path

final_pdb_path: pathlib.Path

summary_log_path: pathlib.Path

class iphasimulator.simulation_openmm_amber_runner.OpenMMStageTimings

Wall-clock timings for an OpenMM AMBER workflow.

minimization_seconds: float

nvt_seconds: float

npt_seconds: float

production_seconds: float

exception iphasimulator.simulation_openmm_amber_runner.OpenMMRunnerError

Raised when OpenMM is unavailable or simulation setup fails.

iphasimulator.simulation_openmm_amber_runner.openmm_available() → bool

Return True when OpenMM can be imported.

iphasimulator.simulation_openmm_amber_runner.run_openmm_with_amber_topology(prmtop_path: str | pathlib.Path, inpcrd_path: str | pathlib.Path, output_dir: str | pathlib.Path, *, temperature_kelvin: float = 300.0, friction_per_picosecond: float = 1.0, timestep_femtoseconds: float = 2.0, minimization_max_iterations: int = 200, simulation_steps: int = 100, nvt_steps: int | None = None, npt_steps: int = 100, production_steps: int = 100, report_interval: int = 10, pressure_bar: float = 1.0, nonbonded_cutoff_nanometers: float = 1.0, platform_name: str | None = None, platform_precision: str | None = 'mixed') → OpenMMOutputs

Run minimization, NVT, NPT when periodic, and production from AMBER files.