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Dataset results
299 results for “MD simulation”
ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 100mM CaCl2, 298K
<p>Simulation data and parameters of ECC-LIPID17 simulation of POPC:POPG 50:50 mixture with Na+ counterions and 100mM CaCl2 at 298K, ran for NMRlipidsIVb:</p> <p>https://github.com/NMRLipids/NMRlipidsIVPEandPG/blob/master/Manuscript/manuscriptPGPE.pdf</p> <p>ECC-ion parameters are from bitbucket.org/hseara/ions/src/master/</p>
LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions, 298K
<p>The last 200ns of a 320ns MD simulation trajectory with Amber lipid 17 force field. POPC:POPG 50:50 (150 POPC, 150 POPG) mixture with Na+ counterions. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx The starting structure was generated by removing appropriate number of POPC lipids to get 50:50 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12.</p>
ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions, 298K
<p>Simulation data and parameters of ECC-LIPID17 simulation of POPC:POPG 50:50 mixture with Na+ counterions at 298K, ran for NMRlipidsIVb:</p> <p>https://github.com/NMRLipids/NMRlipidsIVPEandPG/blob/master/Manuscript/manuscriptPGPE.pdf</p> <p>ECC-ion parameters are from bitbucket.org/hseara/ions/src/master/</p>
ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 1000mM CaCl2, 298K
<p>Simulation data and parameters of ECC-LIPID17 simulation of POPC:POPG 50:50 mixture with Na+ counterions and 1000mM CaCl2 at 298K, ran for NMRlipidsIVb:</p> <p>https://github.com/NMRLipids/NMRlipidsIVPEandPG/blob/master/Manuscript/manuscriptPGPE.pdf</p> <p>ECC-ion parameters are from bitbucket.org/hseara/ions/src/master/</p>
MD simulations of bilayers containing POPC and Cholesterol: 52POPC_76CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (52 POPC, 76 CHL), N_wat/lipid = 31, 24496 Atoms</p>
MD simulations of bilayers containing POPC and Cholesterol: 64POPC_64CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (64 POPC, 64 CHL), N_wat/lipid = 31, 25216 Atoms</p>
MD simulations of bilayers containing POPC and Cholesterol: 84POPC_44CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (84 POPC, 44 CHL), N_wat/lipid = 31, 26416 Atoms</p>
MD simulations of bilayers containing POPC and Cholesterol: 108POPC_20CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (108 POPC, 20 CHL), N_wat/lipid = 31, 27856 Atoms</p>
POPC bilayers from MD simulations run with CHARMM using C36 parameters
<p>DCD trajectory files from MD simulations for aqueous POPC bilayers (no ions) at two sizes: 72 lipids (400 ns), and 648 lipids (200 ns) with frames spaced at 25 ps. Filenames indicate the number of lipids and the time range in nanoseconds. The original literature citation is:</p> <p>Mechanical properties of lipid bilayers from molecular dynamics simulation. Richard M. Venable, Frank L.H. Brown, Richard W. Pastor. Chemistry and Physics of Lipids 192 (2015) 60–74. </p> <p>http://dx.doi.org/10.1016/j.chemphyslip.2015.07.014</p>
MD simulation trajectory and related files for POPC bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field (dx.doi.org/10.1021/jp101759q), 20ns, T=303K, 72 POPC molecules, 2242 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 (dx.doi.org/10.1021/jp101759q).</p>
MD simulation trajectory and related files for POPC bilayer in low hydration (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field in low hydration (dx.doi.org/10.1021/jp101759q), 20ns, T=303K, 72 POPC molecules, 504 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 (dx.doi.org/10.1021/jp101759q).</p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, PME, traj 2)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using PME (Particle Mesh Ewald) for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 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 (dx.doi.org/10.1002/jcc.21396).</p>
MD simulation trajectory for POPC/50% Chol bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC/50%CHL lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 80 POPC/80 Cholesterol at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</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 DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, Reaction Field, traj 1)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using Reaction Field for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 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 (dx.doi.org/10.1002/jcc.21396).</p>
MD simulation trajectory and related files for n-octyl-b-D-maltoside (C8G2) simulation in lamellar phase (Gromacs 4.5.)
<p>Simulation trajectory and related files used in:</p> <p>Signal intensities in 1H–13C CP and INEPT MAS NMR of liquid crystals</p> <p>A. Nowacka, N.A. Bongartz, O.H.S. Ollila, T. Nylander and D. Topgaard</p> <p>Journal of Magnetic Resonance 230 (2013) 165–175</p> <p>http://dx.doi.org/10.1016/j.jmr.2013.02.016</p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, Reaction Field, traj 2)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using Reaction Field for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 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 (dx.doi.org/10.1002/jcc.21396).</p> <p> </p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, PME, traj 1)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using PME (Particle Mesh Ewald) for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 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 (dx.doi.org/10.1002/jcc.21396).</p>
MD simulation trajectory and related files for POPC bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 128 POPC at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</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 for POPC/20% Chol bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC/20%CHL lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 100 POPC/24 Cholesterol at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</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 DPPC bilayer (GAFFlipid, Gromacs 4.5)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.5, GAFFlipid force field (http://dx.doi.org/10.1039/C2SM26007G), 50ns, T=323K, 72 DPPC molecules, 2197 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>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.