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299 results for “MD simulations”
MD simulation trajectory of Ternary mixture of POPC/PSM/Chol (2:2:1) at 295 K: Slipids, GROMACS 5.1.4.
<p>MD simulation trajectory files for Ternary mixture of POPC/PSM/Chol [408 POPC, 408 PSM, 208 Chol and 35840 SOL]. The Slipids (2013 version) force field was used with Gromacs 5.1.4. Conditions: T=295K. Data saved every 20 ps. 100 ns trajectory.</p>
MD simulation trajectory for Heterogenous lipid bilayer with no counter-ions
<p>Equilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, no ions, 19606 water (TIP3P) molecules. </p>
MD simulation trajectory for Heterogenous lipid bilayer with 150mM NaCl concentration
<p>Equilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, 92 Na+, 56 Cl- , 19348 water (TIP3P) molecules. </p>
MD simulation trajectory for Heterogenous lipid bilayer with 150mM CaCl2 concentration
<p>Equilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, 73 Ca2+, 110 Cl2- , 18915 water (TIP3P) molecules. </p>
MD simulation trajectory for Heterogenous lipid bilayer with 150mM CaCl2 concentration
<p>Equilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, 73 Ca2+, 110 Cl2- , 18915 water (TIP3P) molecules. </p>
MD simulation trajectories associated to the publication: Multi-eGO: model improvements towards the study of complex self-assembly processes
<p>The three tgz compressed files include the simulations data and resulting trajectories for the three systems discussed in the work. In particular: </p><ul><li>ab42.tgz includes a random_coil simulation, the multi-eGO simulation of the monomer performed in triplicate and the simulations performed with the original multi-eGO model.</li><li>ttr.tgz includes the randomcoil simulations for both the intramolecular as well as the intermolecular interactions at the three different concentrations, the simulation of the monomer performed in triplicate, and the aggregation kinetics performed in triplicate at the three reported concentrations</li><li>protein_g.tgz includes the reference GB1 simulation, a randomcoil simulation and the 200 multi-eGO folding simulations.</li></ul>
MD simulation of POPC bilayer with OPLS4 force field. 12 w/l.
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MD simulation trajectory and related files for POPC bilayer (GAFFlipid, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, GAFFlipid force field (http://dx.doi.org/10.1039/C2SM26007G), 30ns, T=303K, 126 POPC molecules, 3948 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters: Dickson et al. Soft Matter, 2012,8, 9617-9627 http://dx.doi.org/10.1039/C2SM26007G.</p>
An accurate binding free energy method from end-state MD simulations (ANI_LIE test files)
<p>Required files are added.</p>
MD simulation trajectory and related files for POPC bilayer (Chiu et al. Gromos version, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Chiu et al. force field (http://dx.doi.org/10.1021/jp807056c), 50ns, T=298K, 128 POPC molecules, 3552 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (http://dx.doi.org/10.1021/jp807056c).</p>
KATP MD Simulation Trajectories
<p>MD simulation trajectories of pancreatic KATP channel</p>
MD_simulations_NorA
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MD simulation of DMPC bilayer with OPLS4 force field. 5 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. 10 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. 20 w/l.
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MD simulation of DMPC bilayer with OPLS4 force field. Full hydration.
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MD simulations files for: Structure of the human dopamine transporter in complex with cocaine
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MD Simulations for Alternate Conformational Trajectories in Protein Synthesis
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Data from MD Simulations of MthK and MthK V55E Channels
<p>Data, pdb files and input files underlying our recent publication: https://doi.org/10.1101/2022.03.29.486236 </p>
MD simulations of the Sec61/TRAP/ribosome complex and various subcomplexes with CHARMM36 force field
<p>Simulation data for the Sec61/TRAP/ribosome complex and its subcomplexes (TRAP alone, Sec61 alone, as well as Sec61 with TRAP) embedded in an ER membrane mimic. Simulations are performed using GROMACS and with the all-atom CHARMM family of force fields. The uploaded trajectories (xtc) contain the coordinates stored every 2 ns of the 2-µs-long simulations. The output energy files (edr), run input files (tpr), and the continue points (cpt) at 2 µs are provided. </p> <p>This upload also contains data for the Sec61/TRAP/ribosome complex simulated in a POPC bicelle. This simulation is 1 µs long and the coordinates are stored every 1 ns.</p> <p>All required input files are also provided to regenerate the run input file: initial structures (gro), index files (ndx), topologies (top and itp), and the simulation parameter file (mdp). Details of the setup, simulation, and analysis of the systems is available in the preprint:</p> <p>https://doi.org/10.1101/2022.09.30.510141</p> <p> </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.
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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.