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Dataset results
299 results for “MD simulation”
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 OPLS3e force field, 500 mM NaCl part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl 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_nacl500_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: NaCl</p> <p>Concentration: 500 mM</p> <p>Number of cations: 80</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns of original trajectories)</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 NaCl 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, 100 mM NaCl
<p>MD simulation of POPC bilayer with CHARMM36 force field, 100 mM NaCl</p> <p>Dataset contains simulation files including centered and equilibrated trajectory Nacl100-25-500ns.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: NaCl</p> <p>Concentration: 100 mM</p> <p>Number of cations: 16</p> <p>Simulation time: 500 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 NaCl
<p>MD simulation of POPC bilayer with CHARMM36 force field, 200 mM NaCl</p> <p>Dataset contains simulation files including centered and equilibrated trajectory Nacl200mM-45-500ns.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: NaCl</p> <p>Concentration: 200 mM</p> <p>Number of cations: 32</p> <p>Simulation time: 500 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 NaCl
<p>MD simulation of POPC bilayer with CHARMM36 force field, 1000 mM NaCl</p> <p>Dataset contains simulation files including centered and equilibrated trajectory Nacl1000mM-15-500ns.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: NaCl</p> <p>Concentration: 1000 mM</p> <p>Number of cations: 160</p> <p>Simulation time: 500 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 CHARMM36 force field, 500 mM NaCl
<p>MD simulation of POPC bilayer with CHARMM36 force field, 500 mM NaCl</p> <p>Dataset contains simulation files including centered and equilibrated trajectory Nacl500mM-60-500ns.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: NaCl</p> <p>Concentration: 500 mM</p> <p>Number of cations: 80</p> <p>Simulation time: 500 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, 100 mM NaCl part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl 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_nacl100_x-xns.tar.gz)</p> <p>Dataset also contains Gromacs converted trajectory (.xtc) for the last 500 ns of 1000 ns trajectory</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</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 NaCl part 1</p>
MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 2 (500-1000ns)</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_nacl200_x-xns.tar.gz)</p> <p>Dataset also contains Gromacs converted trajectory (.xtc) for the last 500 ns of 1000 ns trajectory</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Concentration: 200 mM</p> <p>Number of cations: 32</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, 200 mM NaCl 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>
MD simulation trajectory of DOG/SDPE bilayer and related files
<p>Raw simulation trajectory data of pre-equiblirated DOG/SDPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.6 with Lipid17 force field and TIP3P water model. The trajectory is 0-2100 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 12 DOG, 116 SDPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p>
MD simulation trajectory of POPE/SDG/CHOL bilayer and related files
<p>Simulation trajectory pre-equiblirated POPE/SDG/CHOL bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.7 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 74 POPE, 12 SDG, 42 CHOL and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: https://doi.org/10.1016/j.bbamem.2022.183961<br> </p>
MD simulation trajectory of SDPE/SDG/CHOL bilayer and related files
<p>Simulation trajectory pre-equiblirated SDPE/SDG/CHOL bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.7 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 74 SDPE, 12 SDG, 42 CHOL and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a></p>
MD simulation trajectory of POPE/DOG/CHOL bilayer and related files
<p>Simulation trajectory pre-equiblirated POPE/DOG/CHOL bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.7 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 74 POPE, 12 DOG, 42 CHOL and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a></p>
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