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299 results for “MD simulation”
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>
MD simulation trajectory and related files for POPC bilayer with 340mM CaCl_2 (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, 7157 water molecules, 44 Na molecules, 88 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory and related files for POPC bilayer with 950mM NaCl (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 60ns, T=303K, 72 POPC molecules, 2085 water molecules, 37 Na molecules, 37 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory and related files for POPC bilayer with 690mM NaCl (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 60ns, T=303K, 72 POPC molecules, 2085 water molecules, 26 Na molecules, 26 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory for POPC bilayer (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 50ns, T=298K, 72 POPC molecules, 2880 water molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p> <p> </p>
MD simulation trajectory for POPC bilayer with 510mM CaCl_2 (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 60ns, T=298K, 72 POPC molecules, 2802 water molecules, 26 Ca molecules, 52 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory and related files for POPC bilayer with 30 mol% of deprotonated pazePC (Berger, Gromacs 4.5.)
<p>Simulation trajectory and related files for POPC bilayer with 30mol% of pazePC in deprotonated form used in "Acyl chain disorder and azelaoyl orientation in lipid membranes containing oxidised lipids" by T. M. Ferreira, et al., https://doi.org/10.1021/acs.langmuir.6b00788.</p> <p> </p> <p>90 POPC, 38 pazePC, 7250 water and 38 potassium molecules. Simulation time 120ns.</p> <p> </p> <p>Force field for POPC is based on Berger model and force field for pazePC is from H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 – 2743, http://dx.doi.org/10.1016/j.bpj.2009.01.007.</p> <p> </p> <p>If used, please cite approriate publications.</p>
MD simulation trajectory and related files for POPC bilayer with 30 mol% of protonated pazePC (Berger, Gromacs 4.5.)
<p>Simulation trajectory and related files for POPC bilayer with 30mol% of pazePC in deprotonated form used in "Acyl chain disorder and azelaoyl orientation in lipid membranes containing oxidised lipids" by T. M. Ferreira, et al. https://doi.org/10.1021/acs.langmuir.6b00788</p> <p><br> The simulation with deprotonated pazePC from the same publication available at http://dx.doi.org/10.5281/zenodo.44622</p> <p>90 POPC, 38 pazePC, 7250 water and 38 potassium molecules. Simulation time 167ns.</p> <p> </p> <p>Force field for POPC is based on Berger model and force field for pazePC is modified from H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 – 2743, http://dx.doi.org/10.1016/j.bpj.2009.01.007.</p>
MD simulation trajectory for POPC bilayer with 140mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 60ns, T=298K, 72 POPC molecules, 2866 water molecules, 7 Na molecules, 7 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory for POPC bilayer with 510mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 120ns, T=298K, 72 POPC molecules, 2802 water molecules, 26 Na molecules, 26 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory for POPC bilayer with 1000mM NaCl (Orange, Gromacs 4.5.)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Orange, 120ns, T=298K, 72 POPC molecules, 2780 water molecules, 50 Na molecules, 50 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi, https://github.com/NMRLipids/lipid_ionINTERACTION).</p> <p> </p> <p>The Orange model is unpublished lipid model developed by Luca Monticelli et al. http://perso.ibcp.fr/luca.monticelli/research/index.html. Beta version of the model is used here, thus only trajectory is shared.</p>
MD simulation trajectory and related files for POPC bilayer with 670mM CaCl_2 (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 120ns, T=303K, 72 POPC molecules, 2165 water molecules, 26 Ca molecules, 52 Cl molecules.</p> <p>Note! This dataset is NOT used in the NMRLipids II project (nmrlipids.blospot.fi), but the dataset http://dx.doi.org/10.5281/zenodo.35160</p> <p>See also discussion in: https://github.com/NMRLipids/lipid_ionINTERACTION/issues/16</p>
SDS micelle, MD simulation, Gromacs 5.0, CHARMM36
<p>Molecular dynamics simulation of SDS micelle. Gromacs 5.0, CHARMM36. Files generated with CHARMM GUI. System contains 60 SDS molecules, 16854 water molecules and 60 sodium ions. Temperature T=293K. Length is 20ns.</p>
Simulation files for DPPC lipid membrane with Slipids force field for Gromacs MD simulation engine
<p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine
<p>Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine</p> <p>NaCl concentration is 730 mM.</p> <p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
Simulation files for DPPC lipid membrane with Slipids force field for Gromacs MD simulation engine
<p>the files denoted with 350 resp 700 resp 1000 have NaCl concentrations of 850 resp 1750 resp 2570 mM.</p> <p> </p> <p>The goal was to study the effect of salt on the order parameters of the lipid head group and the glycerol backbone for the NMRlipids project, see http://nmrlipids.blogspot.fi for more information.</p>
Snapshots from MD simulations of human beta3 integrin PSI-domain
<p>MD simulation performed with Gromacs 4.0.7</p>
A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria- MD simulation files
<p>This folder contains the first and last frame of MD simulations conducted in this study. </p> <p>The Free-MD folder contains unconstrained MD simulation files for Dri1 (WT) and its variants (H16A, H21A, H79A, H16A:H21A, H16A:H79A, H21A:H79A and H79A:R90A)</p> <p>The SAXS-dirven MD folder contains SAXS data constrained MD simulation files for Dri1 WT, Dri1 H21A and Dri H79A:R90A with 3 different starting structures for variants. </p>
The MD simulation results for the paper "Multifaceted regulation of siderophore synthesis by multiple regulatory systems"
<p>"MD results.zip" contains the initial structures and trajectories, while the other file comprises the input files generated by CHARMM-GUI.”</p>
MD simulation of POPC bilayer with CHARMM36 force field. 7.5 w/l.
<p>MD simulation of POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) bilayer with CHARMM36 force field. 7.5 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: 1500</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>
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International Brain Laboratory public data
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OpenNeuro
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