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1,548
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ShareScore release 0.9.0
Dataset results
1,548 results for “Trajectories”
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=16 w/l
<p>Equilibrated DLPC lipid bilayer ran with Gromacs 4.5.4 with Berger force field, 80ns, T=300K, 72 DLPC molecules, hydration level nw=16 water/lipid.</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p> <p> </p>
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=24 w/l
<p>Equilibrated DLPC lipid bilayer ran with Gromacs 4.5.4 with Berger force field, 80ns, T=300K, 72 DLPC molecules, hydration level nw=24 water/lipid.</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p> <p> </p>
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=20 w/l
<p>Equilibrated DLPC lipid bilayer ran with Gromacs 4.5.4 with Berger force field, 80ns, T=300K, 72 DLPC molecules, hydration level nw=20 water/lipid.</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=8 w/l
<p>Equilibrated DLPC lipid bilayer ran with Gromacs 4.5.4 with Berger force field, 80ns, T=300K, 72 DLPC molecules, hydration level nw=8 water/lipid.</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD simulation trajectory and related files for POPC bilayer with 340mM NaCl (Berger model delivered by Tieleman, ffgmx ions, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Berger force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads), double bonds updated in http://dx.doi.org/10.1021/jp065424f, ffgmx parameters for ions, 50ns, T=298K, 128 POPC molecules, 7202 water molecules, 44 Na molecules, 44 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory and related files for POPC bilayer with 340mM CaCl_2 (Berger model delivered by Tieleman, ffgmx ions, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Berger force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) double bonds updated in http://dx.doi.org/10.1021/jp065424f, ffgmx parameters for ions, 50ns, T=298K, 128 POPC molecules, 7157 water molecules, 44 Na molecules, 88 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory and related files for POPC bilayer with 950mM NaCl (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 60ns, T=303K, 72 POPC molecules, 2085 water molecules, 37 Na molecules, 37 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory and related files for POPC bilayer with 690mM NaCl (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 60ns, T=303K, 72 POPC molecules, 2085 water molecules, 26 Na molecules, 26 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory for POPC bilayer (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 50ns, T=298K, 72 POPC molecules, 2880 water molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p> <p> </p>
MD simulation trajectory for POPC bilayer with 510mM CaCl_2 (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 60ns, T=298K, 72 POPC molecules, 2802 water molecules, 26 Ca molecules, 52 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory and related files for POPC bilayer with 30 mol% of deprotonated pazePC (Berger, Gromacs 4.5.)
<p>Simulation trajectory and related files for POPC bilayer with 30mol% of pazePC in deprotonated form used in "Acyl chain disorder and azelaoyl orientation in lipid membranes containing oxidised lipids" by T. M. Ferreira, et al., https://doi.org/10.1021/acs.langmuir.6b00788.</p> <p> </p> <p>90 POPC, 38 pazePC, 7250 water and 38 potassium molecules. Simulation time 120ns.</p> <p> </p> <p>Force field for POPC is based on Berger model and force field for pazePC is from H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 – 2743, http://dx.doi.org/10.1016/j.bpj.2009.01.007.</p> <p> </p> <p>If used, please cite approriate publications.</p>
MD simulation trajectory and related files for POPC bilayer with 30 mol% of protonated pazePC (Berger, Gromacs 4.5.)
<p>Simulation trajectory and related files for POPC bilayer with 30mol% of pazePC in deprotonated form used in "Acyl chain disorder and azelaoyl orientation in lipid membranes containing oxidised lipids" by T. M. Ferreira, et al. https://doi.org/10.1021/acs.langmuir.6b00788</p> <p><br> The simulation with deprotonated pazePC from the same publication available at http://dx.doi.org/10.5281/zenodo.44622</p> <p>90 POPC, 38 pazePC, 7250 water and 38 potassium molecules. Simulation time 167ns.</p> <p> </p> <p>Force field for POPC is based on Berger model and force field for pazePC is modified from H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 – 2743, http://dx.doi.org/10.1016/j.bpj.2009.01.007.</p>
MD simulation trajectory for POPC bilayer with 140mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 60ns, T=298K, 72 POPC molecules, 2866 water molecules, 7 Na molecules, 7 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory for POPC bilayer with 510mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 120ns, T=298K, 72 POPC molecules, 2802 water molecules, 26 Na molecules, 26 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory for POPC bilayer with 1000mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 120ns, T=298K, 72 POPC molecules, 2780 water molecules, 50 Na molecules, 50 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory and related files for POPC bilayer with 670mM CaCl_2 (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 120ns, T=303K, 72 POPC molecules, 2165 water molecules, 26 Ca molecules, 52 Cl molecules.</p> <p>Note! This dataset is NOT used in the NMRLipids II project (nmrlipids.blospot.fi), but the dataset http://dx.doi.org/10.5281/zenodo.35160</p> <p>See also discussion in: https://github.com/NMRLipids/lipid_ionINTERACTION/issues/16</p>
Myotis nattereri baseline trajectory
<p>Myotis nattereri baseline trajectory x(t), y(t), z(t)</p>
Myotis myotis trajectory by our method
<p>Myotis myotis trajectory by our method x(t), y(t), z(t)</p>
Myotis nattereri trajectory by our method
<p>Myotis nattereri trajectory by our method x(t), y(t), z(t)</p>
Pipistrellus pipistrellus baseline trajectory
<p>Pipistrellus pipistrellus baseline trajectory x(t), y(t), z(t)</p>
ScienceDex guides
Understand access before you commit
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.