MAICoS Data

maicosdata is a data repository for molecular dynamics test datasets used by MAICoS and related projects. It provides curated simulation topologies and trajectories that can be loaded as MDAnalysis Universe objects with a single function call.

maicosdata is open source and released under the GNU General Public License v3.0.

Installation

Install maicosdata using pip:

pip install maicosdata

Quick Start

Fetch a dataset as an MDAnalysis Universe:

import maicosdata

u = maicosdata.fetch("water", in_memory=True)
print(u.atoms.n_atoms)  # 1530

List all available datasets:

maicosdata.list_identifiers()
# ['airwater', 'cntwater', 'kineticenergy', 'mica', 'salt_water', 'slit_flow', 'water']

Read the description of a dataset:

print(maicosdata.describe("airwater"))

You can also access the module through maicosdata.datasets:

from maicosdata import datasets

record = datasets._get_record("water")
print(record.topology)
print(record.trajectory)

Available Datasets

Identifier	Description	Code	Ensemble
airwater	Air-water interface — 264 water molecules at equilibrium with vapor	GROMACS	NVT
cntwater	Carbon nanotube (r = 16 Å) filled with 810 water molecules	LAMMPS	NVT
kineticenergy	Bulk water — 510 TIP3P molecules (NVE kinetic energy data)	GROMACS	NVE
mica	Realistic mica-water interface — two T-O-T slabs with 587 water molecules	GROMACS	NVT
salt_water	Salt water system (topology only)	GROMACS	—
slit_flow	1176 water molecules confined between NaCl walls (topology only)	GROMACS	NVT
water	Bulk water — 510 SPC/E molecules	GROMACS	NVT

Use maicosdata.describe("<identifier>") for full details on any dataset.

API Reference

maicosdata.list_identifiers()

Return a sorted list of all available dataset identifier strings.

maicosdata.describe(identifier)

Return the full-text description (README.rst) for a dataset.

maicosdata.fetch(identifier, **universe_kwargs)

Load a dataset and return an MDAnalysis.Universe. Extra keyword arguments are forwarded to the Universe constructor (e.g., in_memory=True).

Contributing

If you encounter any issues, report them on GitHub, or join our developer community on Discord to discuss features and improvements.