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Dataset results
119 results for “gromacs”
GROMACS simulations of unfolding of ubiqutin in a strong electric field
<p>The simulations were performed in GROMACS 4.6.7. The dataset contains binary run input files (.tpr) and simulated trajectory files (.trr). Here are 100 statistically independent runs for the field values: E = 3e4 V/nm, E = 5e4 V/nm, E = 7e4 V/nm, E = 11e4 V/nm. The names of files denote the value of the electric field in [V/nm] and the number of independent runs.</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>
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=4 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=4 water/lipid. 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=28 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=28 water/lipid.</p>
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=12 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=12 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=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>
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International Brain Laboratory public data
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OpenNeuro
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