Tutorial 8: Hyper Solvate Sumo

What you get: A solvated TRC structure that you can pass directly into minimization or MD.

Time

~2-5 minutes

Skill level

Beginner

Prerequisites

Python 3.12+, rush-py installed, RUSH_TOKEN and RUSH_PROJECT set

Quick Start

from pathlib import Path

from rush import RunOpts, TRC, hyper

input_trc = Path("tests/data/hyper/valid_trc.json")

run = hyper.hyper_solvate_sumo(
    [input_trc],
    config=hyper.HyperConfig(max_inputs=8, padding_nm=0.8, seed=12345, timeout_seconds=120),
    run_opts=RunOpts(name="Tutorial: Hyper Solvate", tags=["rush-py", "tutorial", "hyper", "solvate"]),
)

item = run.fetch()[0]
if not isinstance(item, TRC):
    raise RuntimeError(f"Unexpected per-item error: {item}")

print("Solvated atoms:", len(item.topology.symbols))

Output Contract

hyper_solvate_sumo() returns Run[hyper.TRCBatchResultRef].

  • run.collect() -> TRCBatchResultRef

  • result_ref.fetch() -> list[TRC | ItemError]

  • result_ref.save() -> list[Path | ItemError]

See Also