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Dataset results
220 results for “force fields”
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>
The influence of the choice of force field on the conformational landscape of monomeric rat and human islet amyloid polypeptide
<p>Dataset of the BEMD data used in the paper "The influence of the choice of force field on the conformational landscape of monomeric rat and human islet amyloid polypeptide"</p>
POPG lipid bilayer simulation at T298K ran with MODEL_CHARMM_GUI force field and Gromacs
<p>POPG lipid bilayer simulation at T298K ran 100ns with the force field given by CHARMM gui using Gromacs.</p> <p>118 POPG, 4110 TIP3P and 118 potassium molecules.</p> <p> </p>
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>
MD simulation of POPC bilayer using a force field calibrated to NMR order parameters
<p>Force field parameters and simulation trajectory for 34-lipid bilayer simulation where the force field has been calibrated to reproduce the NMR C-H 13C order parameters. Temperature is 300K, and simulation was conducted in NPT ensemble with asymmetric pressure coupling. The trajectory is 1 microsecond long. The simulation was started from an equilibrated conformation and few tens of nanoseconds of pre-equilibration was run before obtaining the 1 microsecond production run. The trajectory has been centered to the simulation box. The simulations where conducted on GROMACS 2020 (GPU). </p>
Dataset and analyses for: Force-field perturbations and muscle vibration strengthen stability-related foot placement responses during steady-state gait in healthy adults
<p>We have collected kinematic data (heel and pelvis markers) from healthy adults during treadmill walking, whilst force-field perturbations and timed muscle vibrations were applied. We assessed the (after-)effects of these two interventions by evaluating foot placement control through outcome measures derived from a regression model which predicts foot placement based on the center-of-mass kinematic state. The data and analyses provided belong to the scientific publication: "Force-field perturbations and muscle vibration strengthen stability-related foot placement responses during steady-state gait in healthy adults". In the manuscript we place these analyses in the context of stability control and speculate on how these trainining interventions may improve stability control in patient populations.</p>
MD simulation of POPC bilayer with OPLS4 force field. Full hydration
<p>MD simulation of POPC bilayer with OPLS4 force field. Full hydration</p> <p>Dataset contains trajectories (_trj), topologies (-out.cms), input files and converted gromacs format files</p> <p>For the ease of the upload, trajectory file (_trj) is divided into 3 pieces and tarred (named desmond_md_popc_fullhydr_opls4_x-xns.tar.gz)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 9000</p> <p>Simulation time: 500 ns</p> <p>Simulation engine: Desmond 2021-3</p> <p>Temperature: 300 K</p> <p> </p>
Saccharide simulations comparing CHARMM36, CHARMM36-NBFIX, and prosECCo75 force fields, part 4/4 after revisions
<p>Free energy of rotation around the glycosidic bond of (1,4)-D-GalA-D-GalA and (1,4)-D-GlcA-D-GlcNAc with three different force fields.</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>
Simulation of a POPE bilayer at 310K with the CHARMM36 force field
<p>A bilayer of 144 POPE lipids (72 per leaflet) simulated in water (40 molecules per lipid) for 500 ns using the CHARMM36 force field [1] using GROMACS v. 2018.6 [2]. Topologies are obtained from CHARMM-GUI [3].</p> <p>[1] <strong>DOI: </strong>10.1021/jp101759q</p> <p>[2] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p> <p>[3] <strong>DOI: </strong>10.1021/acs.jctc.5b00935</p> <p> </p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.