Datasets:

colabfit
/

MD22_Ac_Ala3_NHMe

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
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PO_1002237494818131681084207	10022374948181316810842072924385267538262668048063287107425305253935677568447559441547217363587502402466255896868547459935680081758691081860864124534875499	2025-04-16T17:42:42	DS_l6awe3jnivnm_0	1	FHI-aims	DFT-PBE+MBE	-26,914.606626	[ [ 0.8147291204947354, 0.9594047803382848, -0.10886081279101022 ], [ -0.7348177498267222, 0.5860268365230068, -0.18778174732593386 ], [ 0.4156804944523845, -0.08951131598952651, -0.7199481985992089 ], [ 0.2517598452977521, -0.5473590650748479, -0.1013167596...	[]	null	null	null	null	null	null	3.611877	1.666761	null	CO_1018957156326196462494479	10189571563261964624944790119150992282169880109007090595873039076298957621091798077400984993669213467483341001488355966493124346709194466203805080487423855	5074084426425060863676374278616288415684891557540006464108559849238572073413318697128453018283812696073734044884521331275637494327719783834984759126254081	[ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]	[ [ -3.92797, 0.743699, 0.531191 ], [ -4.22464, 2.49062, 0.502364 ], [ -3.19805, 1.88873, 1.74071 ], [ -3.44613, 1.76732, 0.659717 ], [ -1.5506, 3.16887, -0.117071 ], [ -2.28937, 2.17941, -0.347573 ], [ -2.16162, 1...	[ false, false, false ]	C12H22N4O4	C6H11N2O2	A11B6C2D2	[ "C", "H", "N", "O" ]	[ 0.2857142857142857, 0.5238095238095238, 0.09523809523809523, 0.09523809523809523 ]	[ 1, 1, 1, 6, 8, 6, 7, 1, 6, 1, 6, 6, 8, 1, 1, 1, 7, 1, 6, 1, 6, 6, 8, 1, 1, 1, 7, 1, 6, 1, 6, 6, 8, 1, 1, 1, 7, 1, 6, 1, 1, 1 ]	42	4	[ 0, 0, 0 ]	[ "md22_Ac-Ala3-NHMe_66896" ]	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 Ac Ala3 NHMe. ColabFit, 2023. https://doi.org/10.60732/4bc7295f

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Dataset Name

MD22 Ac Ala3 NHMe

Description

Dataset containing MD trajectories of the 42-atom tetrapeptide Ac-Ala3-NHMe 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

85099

Number of atoms

3574158

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).