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ShareScore release 0.9.0
Dataset results
4 results for “NAMD trajectories”
NAMD Trajectory of a Palmitoyl Sphingomyelin Bilayer
<p>All-atom PSM bilayer simulated in NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2020 J. Phys. Chem. B. article (DOI 10.1021/acs.jpcb.0c03389). The trajectory represents the last 117 ns used for analysis where the area per lipid is equilibrated (the file has 5874 frames output every 20 ps). The bilayer has 200 lipids total (100 lipids per leaflet) and is hydrated with 45 waters/lipid. The simulation was done at 55C (328.15K) and the trajectory is centered on the bilayer midplane.</p>
NAMD Trajectory of a Tetraoleoyl Cardiolipin Bilayer
<p>All-atom TOCL (tetraoleoyl cardiolipin) bilayer simulated in NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a). The trajectory represents the last 155 ns used for analysis where the area per lipid is equilibrated (the file has 7752 frames output every 20 ps). The bilayer has 100 lipids total (50 lipids per leaflet) and is hydrated with 60 waters/lipid and 140mM NaCl. The simulation was done at 30C (303.15K) and the trajectory is centered on the bilayer midplane.</p>
NAMD Trajectory of a DLiPC (di18:2PC) bilayer
<p>All-atom DLiPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) bilayer simulated in NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a). The trajectory represents the last 245 ns used for analysis where the area per lipid is equilibrated (the file has 12250 frames output every 20 ps). The bilayer has 200 lipids total (100 lipids per leaflet) and is hydrated with 45 waters/lipid. The simulation was done at 25C (298.15K) and the trajectory is centered on the bilayer midplane.</p> <p> </p> <p> </p>
NAMD Trajectory of a POPC/PSM 70/30 bilayer
<p>All-atom bilayer mixture of POPC/PSM 70/30 simulated in an NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a). The trajectory represents the last 126 ns used for analysis where the area per lipid is equilibrated (the file has 3145 frames output every 40 ps). The bilayer has 200 lipids total (100 lipids per leaflet) and is hydrated with 70 waters/lipid and 140mM NaCl. The simulation was done at 25C (298.15K) and the trajectory is centered on the bilayer midplane.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.