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98 results for “lipid bilayer”
Simulations of POPC lipid bilayer in water solution with various molar fractions of cationic surfactant dihexadecylammonium using ECC-POPC force field
<p>Classical molecular dynamics simulations of a POPC lipid bilayer in water solution with various molar fractions of cationic surfactant dihexadecylammonium using ECC-POPC force field parameters, SPC/E water model and ECC-ions.</p> <p>Simulation at pure water is in a separate Zenodo deposit<br> https://doi.org/10.5281/zenodo.1118266</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations)</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 200 ns</p> <p>temperature 313 K (otherwise noted)</p>
Simulations of POPC lipid bilayer in water solution at various NaCl and CaCl2 concentrations using ECC-POPC force field and various water models
<p>Classical molecular dynamics simulations of a POPC lipid bilayer in water solution at various NaCl and CaCl2 concentrations using ECC-POPC force field parameters, various water models and ECC-ions.</p> <p>Simulations with SPC/E water model are in a separate Zenodo deposit<br> https://doi.org/10.5281/zenodo.1118266</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations)</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 300 ns</p> <p>temperature 313 K (otherwise noted)</p>
Live imaging of double supported lipid bilayers upon myelin protein injection
<p>Supplementary information for Krokengen et al. preprint at https://www.biorxiv.org/content/10.1101/2024.07.15.603506v1</p>
Simulation of a POPC bilayer at 298K, lipid model by Maciejewski and Rog
<p>Simulation of a POPC bilayer containing 128 lipids with 40 water molecules per lipid and in the absence of ions at 298 K.</p> <p>The lipid model by Maciejewski and Rog [1,2] was used. Topologies (.itp) were obtained from [2]. TIP3P water was used, and the ions were modelled using default OPLS ion parameters. The simulation is 200 ns long with trajectory saved every 100 ps. Simulations were performed with Gromacs 2016.3 [3]</p> <p>The trajectory (.xtc), energy file (.edr), checkpoint file (.cpt), run input file (.tpr), index file (.ndx), topology file (.top), final structure (gro), and the simulation parameter file (.mdp) are provided. </p> <p>[1] Maciejewski et al., J. Phys Chem. B 118, 2014, pp. 4571–4581, DOI: 10.1021/jp5016627 </p> <p>[2] Kulig et al., Data in Brief 5, 2015, pp. 333–336, DOI: 10.1016/j.dib.2015.09.013</p> <p>[3] Abraham et al., SoftwareX 1–2, 2015, pp. 19–25, DOI: 10.1016/j.softx.2015.06.001</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix).</p> <p>Lipid17 force field parameters used for lipids, TIP3p water model and Dang ions.</p> <p>The file names report the number of additional cations.</p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field and ff99 ions
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix).</p> <p>Lipid17 force field parameters used for lipids, TIP3p water model and ff99 ions.</p> <p>The file names report the number of additional cations.</p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix).</p> <p>Lipid17 force field parameters used for lipids, TIP3p water model and Dang ions.</p> <p>The file names report the number of additional cations.</p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with only Na+ counterions (or with K+ counterions when noted with "_KCl" suffix).</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of CaCl2.</p> <p>The numbers in the file names denote the number of additional Ca2+ cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Coarse-grained simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation
<p>Membranes consisting of 520 phospholipids varying levels of chain unsaturation together with 56 (10 mol%) cholesterol molecules were simulated at 298 K. The phospholipids had either 1 (DOPC), 2 (DLiPC), 4 (DAPC), or 6 (DDPC) double bonds in both of their chains. The Martini force field [1] was used and the membranes were generated using insane [2].</p> <p>The simulations were run for 75 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).</p> <p>The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:</p> <ul> <li>Topology files (top) and molecular definitions (itp)</li> <li>Index files (ndx)</li> <li>A common run parameter file (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 1 ns</li> <li>Energy file (edr) written every 100 ps</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> <p>The files are named LLLL_CG_CHOLXX_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid</li> <li>CG stands for coarse-grained (All atom data in a separate upload)</li> <li>CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)</li> <li>TTT is the temperature</li> <li>FFF is the tile type (see above)</li> </ul> <p>Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section.</p> <p>[1] <strong>DOI: </strong>10.1021/jp071097f</p> <p>[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00209</p> <p>[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p>
Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation
<p>Asymmetric membranes consisting of DOPC, cholesterol, and a lipid with a varying level of unsaturation were simulated at 310 K. The DOPC leaflet consisted of 130 molecules, whereas the other leaflet consisted of either 125 DLiPC with 2 double bonds in both chains, 120 DAPC with 4 double bonds in both chains, or 115 DDPC with 6 double bonds in both chains. These numbers were adjusted to prevent membrane bending. All systems contained 28 molecules (10 mol%) of cholesterol. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2].</p> <p>The simulations were run for 1 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file.</p> <p>The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:</p> <ul> <li>Topology files (top) and molecular definitions (itp)</li> <li>Index files (ndx)</li> <li>A common run parameter file (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 100 ps</li> <li>Energy file (edr)</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> <p>The files are named DOPC_LLLL_AA_CHOLXX_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid paired with DOPC</li> <li>AA stands for all atom (Coarse-grained data in a separate upload)</li> <li>CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)</li> <li>TTT is the temperature</li> <li>FFF is the tile type (see above)</li> </ul> <p>[1] <strong>DOI: </strong>10.1021/jp101759q</p> <p>[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00935</p> <p>[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of NaCl or KCl.</p> <p>The numbers in the file names denote the number of additional cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters are included in this repository in GROMACS format and are also available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field
<p>Classical molecular dynamics simulations of a POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field parameters, SPC/E water model and ECC-ions.</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations)</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 300 ns</p> <p>temperature 313 K (otherwise noted)</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Coarse-grained simulation of a POPC lipid bilayer
<p>A POPC bilayer consisting of 200 lipids and 2250 water beads (10% represented by antifreeze particles) was simulated for 1 microsecond using GROMACS 2019.2. All simulation outputs, as well as topologies (top, itp), index file (ndx) and run input parameters (mdp) are provided.</p>
Four-armed starfish in two lipid bilayer models
<div> <div> <h3>Summary</h3> <p>In Helfrich spontaneous curvature model (HSC) the energy functional to be minimized for equilibrium shapes is $W_H=\int{(H-H_0)^2} da$, under constraints of fixed volume and fixed area, where $H$ is the local mean curvature and $H_0$ is the spontaneous curvature parameter.</p> <p>Here we report an experiment that, by adjusting $H_0$ one may yield a qualitatively similar equilibrium shape to the bilayer couple model (BC). In BC, energy is $W=\int{H^2}da$ (see Ziherl & Svetina, 2005) with mean curvature integral $c=\int{H da}/4\pi$ fixed ( $c=c_0$) as a third constraint (the reference shape is the unit sphere with area $4\pi$ and $H=1$).</p> <p>This record includes datasets/ procedures for the open software Surface Evolver.</p> </div> </div>
Characterizing the molecular mechanisms for flipping charged peptide flanking loops across a lipid bilayer
<p>All simulation input data and analysis tools for regenerating results from the journal paper:</p> <p>S. J. Patel and R. C. Van Lehn. "Characterizing the Molecular Mechanisms for Flipping Charged Peptide Flanking Loops across a Lipid Bilayer." The Journal of Physical Chemistry B <strong>2018</strong> <em>122</em> (45), 10337-10348</p>
Rheology of sliding leaflets in coarse-grained DSPC lipid bilayers accompanying files
<p>Molecular dynamics configuration files accompanying the manuscript<a href="https://arxiv.org/abs/2007.05784"> arXiv:2007.05784</a>, published in Physical Review E.</p>
POPS+83%popc lipid bilayer simulation at T298K ran CHARMM_GUI force field and Gromacs
<p>POPS+83%popc lipid bilayer simulation at T298K ran CHARMM_GUI force field and Gromacs. 100ns long 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>
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