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Dataset results
64 results for “CaCl2”
Lipid17ecc POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution and Na+ counter ions
<p>Lipid17ecc POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution. The initial structure was taken from https://zenodo.org/record/3874378#.X0OfthmEZGF . Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 Na+ ions, 24840 SPCE water molecules, 475 Ca2+ ions and 950 Cl- ions</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded as equilibration time. Saving frequency of 100-300ns.xtc is 20 ps.</p>
MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl<sub>2</sub> part 2 (500-1000ns)</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory, topology (-out.cms) and other files.</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl100_x-xns.tar.gz)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 100 mM</p> <p>Number of cations: 16</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl<sub>2</sub> part 1</p>
MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl<sub>2</sub> part 2</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory and topology (-out.cms).</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl500_x-xns.tar.gz).</p> <p>Dataset also contains Gromacs converted trajectories for the last 500 ns of 1000 ns, and are as 100 ns pieces for analysis since simulation did not equilibrate during 1000 ns.</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 500 mM</p> <p>Number of cations: 80</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl<sub>2</sub> part 1</p>
MD simulation of POPC bilayer with CHARMM36 force field, 100 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 100 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl100mM_x-x.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 100 mM</p> <p>Number of cations: 16</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 50 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 50 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl_x-xns.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 50 mM</p> <p>Number of cations: 8</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 200 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 200 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl200mM_x-x.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 200 mM</p> <p>Number of cations: 32</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl1000mM_x-x.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8726</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 1000 mM</p> <p>Number of cations: 158</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with CHARMM36 force field, 500 mM CaCl2
<p>MD simulation of POPC bilayer with CHARMM36 force field, 500 mM CaCl<sub>2</sub></p> <p>Dataset contains simulation files including centered trajectory files. For the ease of the upload, trajectory files (.xtc) are divided to 100ns pieces (Cacl500mM_x-x.xtc)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 500 mM</p> <p>Number of cations: 80</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: GROMACS 2019.5</p> <p>Temperature: 300 K</p>
MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl<sub>2</sub> part 2</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory, topology (-out.cms), and other files.</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl1000_x-xns.tar.gz)</p> <p>Dataset also contains Gromacs converted trajectories for the last 500 ns of 1000 ns, and are as 100 ns pieces for analysis since simulation did not equilibrate during 1000 ns.</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 1000 mM</p> <p>Number of cations: 160</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl<sub>2</sub> part 1</p>
MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl2 part 1
<p>MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl<sub>2</sub> part 1</p> <p>Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms) and input files (.cfg, .msj, .cms).</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl500_x-xns.tar.gz)</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectories are as 100 ns pieces for analysis since simulation did not equilibrate during 1000 ns.</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 500 mM</p> <p>Number of cations: 80</p> <p>Simulation time: 1000 ns (in this dataset 0-500ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl<sub>2</sub> part 2</p>
MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl2 part 1
<p>MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl<sub>2</sub> part 1 (0-500ns)</p> <p>Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl200_x-xns.tar.gz)</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectories are as 100 ns pieces for analysis since simulation did not equilibrate during 1000 ns.</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 200 mM</p> <p>Number of cations: 32</p> <p>Simulation time: 1000 ns (in this dataset 0-500ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl<sub>2</sub> part 2</p>
Simulations of a POPC lipid bilayer in water solution at various NaCl and CaCl2 concentration with Lipid14, TIP3p and Dang or ECC ions
<p>flat POPC bilayer simulations at various NaCl and CaCl2 concentration</p> <p>modelled with Lipid14 force field, TIP3p water model and Dang or 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>
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>
Simulation data for CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM CaCl2 ("NB-Fix" used), 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. </p> <p>The second from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the default Charmm<br> ion parameters (type CAL) for CaCl_2. The new extra nonbonded parameters were used for trating the calcium bonding (NB-Fix)</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 360 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </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 (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>
Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM CaCl2, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. </p> <p>The fourth from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The scaled ECC-Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the ECC-ions<br> for CaCl_2. The new extra nonbonded parameters (NB-Fix) were removed.</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89.</p> <p>In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here.</p> <p>This is the same scaling as used for ECC-POPC</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 610 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </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>
Pure POPC membrane simulations with 790 mM CaCl2 with the CHARMM-Drude2023 force field (OpenMM)
<p>214.85 ns MD simulation of pure POPC membrane using Charmm-Drude2023 polarizable force field (</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong></p> <p><strong>)</strong></p> <p>.The system contains 128 POPC lipids, 91 CaCl2, and 6400 SWM4 water molecules.</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. Frame saving frequency is 10ps. There are 21485 frames in this trajectory.</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>
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