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Dataset results
299 results for “MD simulation”
MD simulation of POPC bilayer with CHARMM36 force field. 12 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 12 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered ).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2400</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2022.4</p> <p>Temperature: 300 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 20 w/l
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 20 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-20-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 4000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 10 w/l.
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 10 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-50-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. Full hydration
<p>MD simulation of DMPC bilayer with CHARMM36 force field. Full hydration</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered ).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 10000</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of DMPC bilayer with CHARMM36 force field. 5 w/l.
<p>MD simulation of DMPC bilayer with CHARMM36 force field. 5 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered_pbcmol-20-500ns.xtc).</p> <p>System: DMPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 1000</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 314 K</p>
MD simulation of POPC bilayer with OPLS4 force field. 7.5 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS4 force field. 7.5 w/l</p> <p>Dataset contains original desmond trajectories (_trj), topologies (-out.cms), input files (.cfg, .msj, .cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 250ns pieces and tarred (named desmond_md_popc7.5wl_opls4_x-xns_trj.tar.gz)</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top) </p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 1500</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: Desmond 2022-2</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with OPLS4 force field. 10 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS4 force field. 10 w/l</p> <p>Dataset contains original desmond trajectories (_trj), topologies (-out.cms), input files (.cfg, .msj, .cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 250ns pieces and tarred (named desmond_md_popc10_opls4_x-xns_trj.tar.gz)</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top) </p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: Desmond 2022-2</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with OPLS4 force field. 20 w/l
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with OPLS4 force field. 20 w/l</p> <p>Dataset contains original desmond trajectories (_trj), topologies (-out.cms), input files (.cfg, .msj, .cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 250ns pieces and tarred (named desmond_md_popc20_opls4_x-xns_.tar.gz)</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top) </p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 4000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: Desmond 2022-2</p> <p>Temperature: 300 K</p> <p> </p>
MD simulations associated to the paper "Unveiling An Unexpected Redox Regulation of the Folding, Function and Inhibition in the PTB Domain of FRS2"
<p>This dataset contains the molecular dynamics input files and trajectories performed for the paper "Unveiling An Unexpected Redox Regulation of the Folding, Function and Inhibition in the PTB Domain of FRS2"<br><br>The data are organized in three folders:</p> <ol> <li>`input_files`, which contains the gromacs .mdp files used for all the minimization, equilibration, and run phases.</li> <li>`topologies`, which contains a gromacs topology file (.top) and initial configuration (.gro) for both the oxidized and reduced form of PTB.</li> <li>`MD`, which contains the three 1-µs long trajectories in gromacs compressed format (.xtc) and a reference run file (.tpr) for both the oxidized and reduced form of PTB.</li> </ol>
MD simulations of water systems for On the Path to Optimal Alchemistry
<p>These are the water simulation files (input and output) for the article.</p>
Trajectories of all MD simulations performed of Spike RBD/hACE2 complexes (WT, Delta, BA.1 to BA.4)
<p>Trajectories (.dcd) of the molecular dynamics simulations performed on Spike RBD / hACE2 complexes</p> <p>Protein structure files (.psf) prepared with Charmm36m topology / parameters</p> <p>For the WT (SARS-CoV-2 original strain), 6 additional replicas were uploaded, 3 including all glycans present on both spike and hACE2 et 3 replicas without glycan as control simulations.</p> <p> </p>
EXO5 common haplotypes MD simulation data
<p>Molecular Dynamics simulation data for WT, G172V, L151P and G172V+D115N EXO5, bound to a single-strand DNA, as found in PDB 7LW9. .gro, .pdb, .top and .tpr files are provided for the starting structure, along with compressed .xtc trajectories for all simulation replicas, and an .mdp file with the simulation parameters. The trajectories do not include the first 960 ns of simulation, considered as the equilibration cutoff. The .xtc files contain one frame per 100 ps, with all molecules and atoms except water.</p>
MD simulations from Jephthah et al., 2021
<p>Simulations analyzed in:</p> <p>Jephthah, Stéphanie, et al. ‘Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity’. Journal of Chemical Theory and Computation, vol. 17, no. 10, Oct. 2021, pp. 6634–46. ACS Publications, https://doi.org/10.1021/acs.jctc.1c00408.</p>
Associative bond swaps in MD: simulations data for figure 4
<p>Simulations data</p>
Associative bond swaps in MD: simulations data for figure 3
<p>Simulations data.</p>
MD simulation of POPC bilayer with CHARMM36 force field. 5 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 5 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc and equilibrated and centered centered-350-1000ns.xtc).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 1000</p> <p>Simulation time: 1000 ns</p> <p>Sampling rate: 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field. 10 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 10 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered-75-500ns.xtc).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 2000</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field. Full hydration 44 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. Full hydration 44 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc and equilibrated and centered centered-40-500ns.xtc).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field. 20 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 20 w/l.</p> <p>Dataset contains simulation files including trajectories (.xtc) (original production.xtc, and equilibrated and centered centered-pbcmol-100-500ns.xtc).</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 4000</p> <p>Simulation time: 500 ns</p> <p>Sampling rate: every 10 ps</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl<sub>2</sub> part 2 (500-1000ns)</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory, topology (-out.cms) and other files.</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl100_x-xns.tar.gz)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 100 mM</p> <p>Number of cations: 16</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl<sub>2</sub> part 1</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.