Datasets:

colabfit
/

MD22_DHA

property_id string	property_hash string	last_modified timestamp[us]	dataset_id string	multiplicity int32	software string	method string	energy float64	atomic_forces list	cauchy_stress list	cauchy_stress_volume_normalized bool	electronic_band_gap float64	electronic_band_gap_type string	formation_energy float64	adsorption_energy float64	atomization_energy float64	max_force_norm float64	mean_force_norm float64	energy_above_hull float64	configuration_id string	configuration_hash string	structure_hash string	cell list	positions list	pbc list	chemical_formula_hill string	chemical_formula_reduced string	chemical_formula_anonymous string	elements list	elements_ratios list	atomic_numbers list	nsites int32	nelements int32	dimension_types list	names list	labels list	property_metadata_path string	configuration_metadata_path string	hash string	configuration_metadata string	property_metadata string
PO_1000082083592767107204986	10000820835927671072049863087421090668318147461527927002976177984375235082463770766326374154251856137646341220488604031217035679245663256481833597059374063	2025-04-16T16:30:05	DS_xwmthngerf71_0	1	FHI-aims	DFT-PBE+MBE	-27,383.815915	[ [ -0.09678000708534396, 0.4156518741438101, -0.009055335540625778 ], [ 1.2635215774035349, 0.11843300508602717, -1.1571407577145998 ], [ -0.37469664621489485, -1.9324475713533058, 0.743850492669216 ], [ 0.8529155503895979, 0.4478211009814262, 1.55115134216...	[]	null	null	null	null	null	null	3.873067	1.539915	null	CO_1246898493140833441660515	12468984931408334416605152468170697021006622101666976697517428604589270547124034663659373369634669877799524622089170723727557911711348741810320084611503715	3572953540509501825368750510381959513065142331836808849233777512829261904127744742456753687503473212176783585707064548250148141114863717324717266679556628	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ -2.85994, -2.71499, -7.69191 ], [ -1.02895, -1.81612, -8.66317 ], [ -2.49812, -1.02776, -5.52405 ], [ -2.27073, -1.34054, -2.3585 ], [ -1.03516, -0.131275, 0.468154 ], [ -0.187789, 0.740658, 3.21403 ], [ -2.29291, ...	[ false, false, false ]	C22H32O2	C11H16O	A16B11C	[ "C", "H", "O" ]	[ 0.39285714285714285, 0.5714285714285714, 0.03571428571428571 ]	[ 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ]	56	3	[ 0, 0, 0 ]	[ "md22_DHA_45597" ]	null	data/MD/1358/MD_7974084108286216484751358.json	null	null	null	{"basis-set": "tight", "thermostat": "Nos\u00e9-Hoover, effective mass=1700/cm", "hash": "7974084108286216484751358808541391562734163811575051331827019134340491167742077760478988627567517082202851378696416061922920194545002855666386174232389587", "id": "MD_7974084108286216484751358"}
PO_1000040948796169107980890	10000409487961691079808906016400672026666015058918058280284776509292156569403188988996523911587143519884247448591488724269503301517699952813452199648424137	2025-04-16T17:23:25	DS_xwmthngerf71_0	1	FHI-aims	DFT-PBE+MBE	-27,384.270586	[ [ -0.78873667661672, -2.026955299394259, 0.9634810061049404 ], [ 1.5972257025601602, 0.7247399320802245, -2.02777488095798 ], [ -0.22576566685558044, -0.4837222426007273, 1.9811194415713316 ], [ 0.20142322713098246, -1.5631545261254638, -0.7000223928568864...	[]	null	null	null	null	null	null	3.219741	1.490727	null	CO_1315090261410844261000855	1315090261410844261000855411232365851916054425687492611432073759736950819052336657401301738784763890526766361237254605094827873193416798957792335917304998	5480226535703476933391772299243138712857319231870691790854579997980631480339820736158556239769451608396843606726503280163673710541471004025212374036028982	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ -0.51413, -3.48083, -4.91058 ], [ -1.95021, -4.61731, -3.31138 ], [ -1.57705, -1.22206, -3.71948 ], [ -3.47829, 0.68117, -2.06416 ], [ -1.28048, 2.92098, -2.54235 ], [ 0.161037, 2.18104, 0.0287859 ], [ -1.0552, ...	[ false, false, false ]	C22H32O2	C11H16O	A16B11C	[ "C", "H", "O" ]	[ 0.39285714285714285, 0.5714285714285714, 0.03571428571428571 ]	[ 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ]	56	3	[ 0, 0, 0 ]	[ "md22_DHA_48970" ]	null	data/MD/1358/MD_7974084108286216484751358.json	null	null	null	{"basis-set": "tight", "thermostat": "Nos\u00e9-Hoover, effective mass=1700/cm", "hash": "7974084108286216484751358808541391562734163811575051331827019134340491167742077760478988627567517082202851378696416061922920194545002855666386174232389587", "id": "MD_7974084108286216484751358"}
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PO_1000223589321006382006736	10002235893210063820067362657889282023336315228918464879844886944468534276143446918567968414054472407521944379200452093395866322484759404494250799521058012	2025-04-16T16:07:38	DS_xwmthngerf71_0	1	FHI-aims	DFT-PBE+MBE	-27,383.051888	[ [ 0.3949706657115392, -0.09916546644091559, 0.5143850004688367 ], [ -0.6628853742764182, 0.02747363157494814, -0.3576133574832562 ], [ -0.37369797090206425, -0.4605397926554702, -1.3333941580185609 ], [ -1.0760628926516604, 0.290206459816018, -2.2625004389...	[]	null	null	null	null	null	null	4.19395	1.654552	null	CO_6625815801203321240093243	662581580120332124009324351142451854898005760452763898801608133519997301654112094421698585488812685186388637491931755647060196237261641641666724638624938	2696668228185953395963965852717184008049482724756598648537098044514709912005991107864901500069732534377954855401921686120851992264264763381181289843140828	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ -1.75342, -3.28563, -5.60151 ], [ -0.557421, -2.87791, -3.71278 ], [ -2.00844, -0.53473, -3.20976 ], [ 0.750584, 1.07044, -2.12888 ], [ -1.4624, 1.21276, 0.192539 ], [ -2.77399, 0.293009, 3.18584 ], [ -2.65506, ...	[ false, false, false ]	C22H32O2	C11H16O	A16B11C	[ "C", "H", "O" ]	[ 0.39285714285714285, 0.5714285714285714, 0.03571428571428571 ]	[ 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ]	56	3	[ 0, 0, 0 ]	[ "md22_DHA_41798" ]	null	data/MD/1358/MD_7974084108286216484751358.json	null	null	null	{"basis-set": "tight", "thermostat": "Nos\u00e9-Hoover, effective mass=1700/cm", "hash": "7974084108286216484751358808541391562734163811575051331827019134340491167742077760478988627567517082202851378696416061922920194545002855666386174232389587", "id": "MD_7974084108286216484751358"}
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Cite this dataset
Chmiela, S., Vassilev-Galindo, V., Unke, O. T., Kabylda, A., Sauceda, H. E., Tkatchenko, A., and Müller, K. MD22 DHA. ColabFit, 2023. https://doi.org/10.60732/9d9083b8

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Dataset Name

MD22 DHA

Description

Dataset containing MD trajectories of DHA (docosahexaenoic acid) from the MD22 benchmark set. MD22 represents a collection of datasets in a benchmark that can be considered an updated version of the MD17 benchmark datasets, including more challenges with respect to system size, flexibility and degree of non-locality. The datasets in MD22 include MD trajectories of the protein Ac-Ala3-NHMe; the lipid DHA (docosahexaenoic acid); the carbohydrate stachyose; nucleic acids AT-AT and AT-AT-CG-CG; and the buckyball catcher and double-walled nanotube supramolecules. Each of these is included here in a separate dataset, as represented on sgdml.org. Calculations were performed using FHI-aims and i-Pi software at the DFT-PBE+MBD level of theory. Trajectories were sampled at temperatures between 400-500 K at 1 fs resolution.

Dataset authors

Stefan Chmiela, Valentin Vassilev-Galindo, Oliver T. Unke, Adil Kabylda, Huziel E. Sauceda, Alexandre Tkatchenko, Klaus-Robert Müller

Publication

https://doi.org/10.1126/sciadv.adf0873

Original data link

http://sgdml.org/

License

CC0-1.0

Number of unique molecular configurations

69744

Number of atoms

3905664

Elements included

C, H, O

Properties included

energy, atomic forces

Usage

ds.parquet : Aggregated dataset information.
co/ directory: Configuration rows each include a structure, calculated properties, and metadata.
cs/ directory : Configuration sets are subsets of configurations grouped by some common characteristic. If cs/ does not exist, no configurations sets have been defined for this dataset.
cs_co_map/ directory : The mapping of configurations to configuration sets (if defined).