Datasets:

colabfit
/

MD22_AT_AT_CG_CG

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_1000055646073625527989717	10000556460736255279897174972710167123579886700213082754385722450049757528748582405869236763750873320089165899357531326444492115706670246059004475491297420	2025-04-16T20:25:58	DS_rx1ei5q0x9gy_0	1	FHI-aims	DFT-PBE+MBE	-101,037.065184	[ [ 1.442689045489616, 0.18230052459289886, 0.8878193176191854 ], [ -0.4672395467081119, 0.06984396030645147, 0.6862456170476678 ], [ 0.04130769136541929, -0.8066373787068848, 1.3140581040892865 ], [ 1.82895480098415, 0.013014087949814833, -0.485773364715225...	[]	null	null	null	null	null	null	4.54193	1.562148	null	CO_1107087326764111441434947	1107087326764111441434947007248758233708761303245787626623258924457909835097850534960714506929467532837024716733243339112047080619376517414271835837963718	11419758666263723843168816409502199441459027896156192951552220046061458409285225019881584796825101289805637826654526346786655589966336521240980789544944698	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ 1.11251, 2.05014, -11.3192 ], [ 5.61422, 3.48381, -10.4961 ], [ 3.37236, 2.82726, -10.8687 ], [ 1.98734, 2.8094, -10.4872 ], [ 1.57156, 3.56555, -9.48293 ], [ 2.51068, 4.2449, -8.84657 ], [ 3.90742, 4.14909, ...	[ false, false, false ]	C38H42N30O8	C19H21N15O4	A21B19C15D4	[ "C", "H", "N", "O" ]	[ 0.3220338983050847, 0.3559322033898305, 0.2542372881355932, 0.06779661016949153 ]	[ 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 6, 7, 6, 6, 6...	118	4	[ 0, 0, 0 ]	[ "md22_AT-AT-CG-CG_3798" ]	null	data/MD/1651/MD_8281391655852507181021651.json	null	null	null	{"basis-set": "tight", "thermostat": "Global Langevin, friction coefficient=2 fs", "hash": "8281391655852507181021651451775545115817136549826629050555617405472179359304477687290202011944677652222812824403516856758857563949795073525240270183544203", "id": "MD_8281391655852507181021651"}
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PO_1000661174731535297016282	10006611747315352970162820350576749575707053092575349322122701239873441272244871083754787526924752878132819035804797216714075299695225221910595420571656037	2025-04-16T21:12:08	DS_rx1ei5q0x9gy_0	1	FHI-aims	DFT-PBE+MBE	-101,036.223747	[ [ -0.16784033050620706, 2.799768677058681, 1.0237180828332546 ], [ -0.44655920555791895, -0.6143739512428247, 0.3351685309453481 ], [ 0.22596947814391327, -1.773526803378412, -2.2405582023878012 ], [ 0.570827718105849, 0.17639390000059904, 1.42788454041795...	[]	null	null	null	null	null	null	4.925147	1.672229	null	CO_6506276419710033672319358	6506276419710033672319358636439749391468812132773090333733128850886926227393292859903613604668696829696840109176725602954275383131185914504224089176912762	4651270734499740737443744540682296328294924912859243356979954267559716731154920112684868804438816463399035957902489979679834625453007538343460565693361731	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ 1.86544, 0.320936, -12.042 ], [ 5.58689, 3.18379, -12.1714 ], [ 3.7385, 1.79829, -11.7522 ], [ 2.35579, 1.5717, -11.6525 ], [ 1.58423, 2.46515, -10.9934 ], [ 2.36636, 3.52471, -10.5173 ], [ 3.65014, 3.99337, ...	[ false, false, false ]	C38H42N30O8	C19H21N15O4	A21B19C15D4	[ "C", "H", "N", "O" ]	[ 0.3220338983050847, 0.3559322033898305, 0.2542372881355932, 0.06779661016949153 ]	[ 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 6, 7, 6, 6, 6...	118	4	[ 0, 0, 0 ]	[ "md22_AT-AT-CG-CG_2765" ]	null	data/MD/1651/MD_8281391655852507181021651.json	null	null	null	{"basis-set": "tight", "thermostat": "Global Langevin, friction coefficient=2 fs", "hash": "8281391655852507181021651451775545115817136549826629050555617405472179359304477687290202011944677652222812824403516856758857563949795073525240270183544203", "id": "MD_8281391655852507181021651"}
PO_1000774219643980947811020	10007742196439809478110208950320801581471196564842759265876379059847813996894106637189745250720495988026603524708839080814046934499583155043255508718635539	2025-04-16T18:16:00	DS_rx1ei5q0x9gy_0	1	FHI-aims	DFT-PBE+MBE	-101,036.106825	[ [ 2.623480585471599, -4.300552612543922, -2.1276033845475357 ], [ -0.8916223495312674, 1.069146318079516, 0.09821275707821954 ], [ -0.5128802660634862, 1.0851997093435155, 1.4767168578204115 ], [ -0.13317896861742387, 4.516414785350684, 1.435529631935628 ...	[]	null	null	null	null	null	null	5.468464	1.863099	null	CO_1680740875314334488670469	1680740875314334488670469815558046718186036872516295082518363518797106636394050740278773316529037179205384027929488729245906488956316998413749948860775193	4908354959300743367148969212002328679715237981313759687522854895306868970603977358147471862721844445784049641792705538949446401899529167838002142218966838	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ 0.785589, 3.83009, -10.686 ], [ 5.25597, 2.93798, -9.37892 ], [ 3.1082, 3.53385, -10.0716 ], [ 1.90836, 4.16019, -10.022 ], [ 1.80605, 5.38068, -9.34916 ], [ 2.83875, 5.55665, -8.56972 ], [ 4.08111, 4.90831, ...	[ false, false, false ]	C38H42N30O8	C19H21N15O4	A21B19C15D4	[ "C", "H", "N", "O" ]	[ 0.3220338983050847, 0.3559322033898305, 0.2542372881355932, 0.06779661016949153 ]	[ 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 6, 7, 6, 6, 6...	118	4	[ 0, 0, 0 ]	[ "md22_AT-AT-CG-CG_4298" ]	null	data/MD/1651/MD_8281391655852507181021651.json	null	null	null	{"basis-set": "tight", "thermostat": "Global Langevin, friction coefficient=2 fs", "hash": "8281391655852507181021651451775545115817136549826629050555617405472179359304477687290202011944677652222812824403516856758857563949795073525240270183544203", "id": "MD_8281391655852507181021651"}
PO_1000904625974140936560606	10009046259741409365606063430191049594993498258612093081647610212945169461056896635206953909871027818070006953637683721980744348709820527942955641691112641	2025-04-16T20:29:44	DS_rx1ei5q0x9gy_0	1	FHI-aims	DFT-PBE+MBE	-101,037.471912	[ [ -0.5109115357463992, 0.40237205096529244, -1.167964438048188 ], [ 1.235447656538291, -1.5735532382408264, 0.6895629709960632 ], [ -1.2301268809896881, 0.37003023499415194, -2.258610678841618 ], [ 1.0042866278753988, -0.6793463881170835, 1.177400467056957...	[]	null	null	null	null	null	null	6.077774	1.725128	null	CO_1319624863243833744795277	13196248632438337447952779839176807514048316293235304695673255798388125537821301341166420377689193782302576960806950601706295007539506067517790411694225618	5814665064274223128229949377077063649280871157387576062468313443676788135642330744194725159720755160200763567616488778233015925819005891295410192275318072	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ 3.76064, 1.03207, -4.39281 ], [ 1.5555, 4.15957, -7.2219 ], [ 2.87705, 2.65417, -5.86115 ], [ 3.39828, 1.40025, -5.69205 ], [ 3.64437, 0.557662, -6.68172 ], [ 3.28604, 1.0413, -7.91895 ], [ 2.63031, 2.22044, ...	[ false, false, false ]	C38H42N30O8	C19H21N15O4	A21B19C15D4	[ "C", "H", "N", "O" ]	[ 0.3220338983050847, 0.3559322033898305, 0.2542372881355932, 0.06779661016949153 ]	[ 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 6, 7, 6, 6, 6...	118	4	[ 0, 0, 0 ]	[ "md22_AT-AT-CG-CG_9575" ]	null	data/MD/1651/MD_8281391655852507181021651.json	null	null	null	{"basis-set": "tight", "thermostat": "Global Langevin, friction coefficient=2 fs", "hash": "8281391655852507181021651451775545115817136549826629050555617405472179359304477687290202011944677652222812824403516856758857563949795073525240270183544203", "id": "MD_8281391655852507181021651"}
PO_1000955565867408494145692	10009555658674084941456923203844182590352709548690436305794255175372038442741414620634355944011018463919565551601623982685666532588400019683179977007756768	2025-04-16T15:41:31	DS_rx1ei5q0x9gy_0	1	FHI-aims	DFT-PBE+MBE	-101,037.144132	[ [ -1.1153030702713074, 0.12278589383556872, -2.2511607257914954 ], [ 1.1017301057504216, -0.880772650735339, -1.1772920567972054 ], [ 2.209284010654693, -1.5087108936782692, -1.110741166540965 ], [ -2.423402946484652, 2.132382108797381, 1.113156547128228 ...	[]	null	null	null	null	null	null	4.359019	1.704599	null	CO_1168605307857125829251737	11686053078571258292517373378807063630709128653242647025778312379962299814583911201772413912218280589317970484439162333915536284506385224927262891725055920	7564500992729956864230023323464612092317990658274797724228412872022443303857411118873077454541271839230807626796371344478545502801109673934219980278472334	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ 1.09525, 4.40761, -8.01344 ], [ 5.14473, 3.00807, -9.5463 ], [ 3.11983, 3.6813, -8.75532 ], [ 2.28849, 3.82431, -7.75108 ], [ 2.5088, 3.68945, -6.47525 ], [ 3.73215, 3.30938, -6.19872 ], [ 4.78612, 2.98696, ...	[ false, false, false ]	C38H42N30O8	C19H21N15O4	A21B19C15D4	[ "C", "H", "N", "O" ]	[ 0.3220338983050847, 0.3559322033898305, 0.2542372881355932, 0.06779661016949153 ]	[ 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 6, 7, 6, 6, 6...	118	4	[ 0, 0, 0 ]	[ "md22_AT-AT-CG-CG_5683" ]	null	data/MD/1651/MD_8281391655852507181021651.json	null	null	null	{"basis-set": "tight", "thermostat": "Global Langevin, friction coefficient=2 fs", "hash": "8281391655852507181021651451775545115817136549826629050555617405472179359304477687290202011944677652222812824403516856758857563949795073525240270183544203", "id": "MD_8281391655852507181021651"}
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PO_1002084975511121390439706	1002084975511121390439706440108264570705053277836830333284288966782079227698343195074747208834784879247917686200755609833121332935430431203376655152621302	2025-04-17T17:35:57	DS_rx1ei5q0x9gy_0	1	FHI-aims	DFT-PBE+MBE	-101,036.460589	[ [ -0.479017237327513, -1.9882528366629793, -0.7508451226283817 ], [ 0.35060788649811536, -1.4212411597003825, -0.14099404742238877 ], [ -1.3620448214656828, 0.5451171409031873, -0.15773129060490076 ], [ 0.18150219144008894, 0.7292237804235456, 0.4862893975...	[]	null	null	null	null	null	null	6.708671	1.677532	null	CO_5058942573008173818528056	5058942573008173818528056985484972812114054433738369037361603624114202525961761274888334660865304792585852555665140516122416395284178393718743482332260344	10289644608757767956632645759044511246398740768330254094234789033562444302342763896260264106388013081952338398415484518806192112002605810152814478635491594	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ 3.40611, 2.57777, -11.107 ], [ 7.37353, 0.755126, -9.46895 ], [ 5.37081, 1.63256, -10.262 ], [ 4.53747, 2.73933, -10.4188 ], [ 4.7038, 4.01683, -9.93325 ], [ 5.9812, 4.02897, -9.43991 ], [ 6.98296, 3.03488, ...	[ false, false, false ]	C38H42N30O8	C19H21N15O4	A21B19C15D4	[ "C", "H", "N", "O" ]	[ 0.3220338983050847, 0.3559322033898305, 0.2542372881355932, 0.06779661016949153 ]	[ 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 8, 7, 6, 7, 6, 6, 6, 7, 6, 7, 1, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 6, 6, 1, 1, 1, 1, 1, 7, 6, 7, 6, 6, 6...	118	4	[ 0, 0, 0 ]	[ "md22_AT-AT-CG-CG_751" ]	null	data/MD/1651/MD_8281391655852507181021651.json	null	null	null	{"basis-set": "tight", "thermostat": "Global Langevin, friction coefficient=2 fs", "hash": "8281391655852507181021651451775545115817136549826629050555617405472179359304477687290202011944677652222812824403516856758857563949795073525240270183544203", "id": "MD_8281391655852507181021651"}

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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 AT AT CG CG. ColabFit, 2023. https://doi.org/10.60732/a87c6d4c

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Dataset Name

MD22 AT AT CG CG

Description

Dataset containing MD trajectories of AT-AT-CG-CG DNA base pairs 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

10153

Number of atoms

1198054

Elements included

C, H, N, 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).