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220
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ShareScore release 0.9.0
Dataset results
220 results for “force fields”
Amyloid-beta 16-22 peptide monomer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 2)
<p>Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. Initial structures are obtained from CHARMM-GUI. This is the second independent simulation run out of three. The system does not contain any ions.</p> <p>Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p> <p> </p>
Amyloid-beta 16-22 peptide dimer simulation (150 mM NaCl) with the CHARMM-Drude force field and OpenMM (Run 1)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 150 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the first out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p> <p>The trajectory is divided into 7 parts: part_1-2 are each 200 ns long; part_3-6 are each 100 ns long, and part_7 is 640 ns long. Frames are saved in every 10 ps.</p>
Amyloid-beta 16-22 peptide dimer simulation (150 mM NaCl) with the CHARMM-Drude force field and OpenMM (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 150 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the third out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p> <p>The trajectory is divided into 7 parts: part_1-2 are each 200 ns long; part_3-6 are each 100 ns long, and part_7 is 640 ns long. Frames are saved in every 10 ps.</p>
Amyloid-beta 16-22 peptide dimer simulation (150mM NaCl) with the CHARMM36m force field and Gromacs (Run 2)
<p>Amyloid-beta 16-22 peptide dimer simulation with the CHARMM36m force field. This directory contains the second of the three independent trajectories and the simulation length is 1 microseconds. The system contains two amyloid-beta 16-22 monomers, 30 Na+, 30 Cl-, and 10564 TIP3P water.</p>
Amyloid-beta 16-22 peptide dimer simulation (150mM NaCl) with the CHARMM36m force field and Gromacs (Run 1)
<p>Amyloid-beta 16-22 peptide dimer simulation with the CHARMM36m force field. This directory contains first of the three independent trajectories and the simulation length is 1 microseconds. The system contains two amyloid-beta 16-22 monomers, 30 Na+, 30 Cl-, and 10564 TIP3P water.</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>
MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl<sub>2</sub> part 2</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory and topology (-out.cms).</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl500_x-xns.tar.gz).</p> <p>Dataset also contains Gromacs converted trajectories for the last 500 ns of 1000 ns, and are as 100 ns pieces for analysis since simulation did not equilibrate during 1000 ns.</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: 500 mM</p> <p>Number of cations: 80</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, 500 mM CaCl<sub>2</sub> part 1</p>
MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 2</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_nacl500_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: NaCl</p> <p>Concentration: 500 mM</p> <p>Number of cations: 80</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns of original trajectories)</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, 500 mM NaCl part 1</p>
MD simulation of POPC bilayer with CHARMM36 force field, 100 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 100 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl100mM_x-x.xtc)</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</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 50 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 50 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl_x-xns.xtc)</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: 50 mM</p> <p>Number of cations: 8</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 200 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 200 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl200mM_x-x.xtc)</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: 200 mM</p> <p>Number of cations: 32</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl1000mM_x-x.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8726</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 1000 mM</p> <p>Number of cations: 158</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 100 mM NaCl
<p>MD simulation of POPC bilayer with CHARMM36 force field, 100 mM NaCl</p> <p>Dataset contains simulation files including centered and equilibrated trajectory Nacl100-25-500ns.xtc.</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: NaCl</p> <p>Concentration: 100 mM</p> <p>Number of cations: 16</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 200 mM NaCl
<p>MD simulation of POPC bilayer with CHARMM36 force field, 200 mM NaCl</p> <p>Dataset contains simulation files including centered and equilibrated trajectory Nacl200mM-45-500ns.xtc.</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: NaCl</p> <p>Concentration: 200 mM</p> <p>Number of cations: 32</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM NaCl
<p>MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM NaCl</p> <p>Dataset contains simulation files including centered and equilibrated trajectory Nacl1000mM-15-500ns.xtc.</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: NaCl</p> <p>Concentration: 1000 mM</p> <p>Number of cations: 160</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 500 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 500 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl500mM_x-x.xtc)</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: 500 mM</p> <p>Number of cations: 80</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</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
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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.