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299 results for “MD simulations”
MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 1000 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_nacl1000_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: 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 NaCl part 1</p>
MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl2 part 1
<p>MD simulation of POPC bilayer with OPLS3e force field, 1000 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_cacl1000_x-xns.tar.gz).</p> <p>Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectories is also for the first 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 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, 1000 mM CaCl<sub>2</sub> part 2</p>
Molecular basis of human norepinephrine transporter reuptake and inhibition - MD simulation files
<p>Molecular Simulation Data Associated with the Manuscript</p> <p>The "simulation system" folder contains the simulation parameters for the LDP and LNR small molecules, as well as the construction files for the two simulation systems.</p> <p>The "equilibrium" and "production" folders contain the coordinates and parameters related to the pre-equilibrium and production of the two simulation systems.</p> <p>LDP: NET-DA</p> <p>LNR: NET-NE</p>
MD simulation of POPC bilayer with OPLS4 force field. 5 w/l
<p>MD simulation of POPC bilayer with OPLS4 force field. 5w/l</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 4 pieces and tarred (named <span>desmond_md_popc</span>_5wl_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: 1000</p> <p>Simulation time: 1000 ns</p> <p>Simulation engine: Desmond 2022-2</p> <p> </p> <p>Temperature: 300 K</p>
MD simulation trajectory for POPC bilayer with 128 lipid molecules (CHARMM36, Gromacs 5.1)
<p>Equilibrated POPC lipid bilayer ran with Gromacs 5.1.2 with CHARMM36 lipid forcefield.<br> The simulation is composed of 128 POPC at full hydratation and ran for 500ns at 303K, data saved every 10ps.<br> This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
The P-V-T dataset of liquid Fe-C alloys from FP-MD simulations
<p><span>The <em>P</em>-<em>V</em>-<em>T</em></span><span> </span><span>dataset </span><span>of</span><span> liquid </span><span>Fe-C</span><span> alloys with different carbon contents (<em>X</em><sub>C</sub> = 0, 2.1, 4.7, 7.6, and 11.2 wt%) under the <em>P</em>-<em>T</em> conditions of the outer core (~136-330 GPa, 4000-6000 K) are obtained via first-principles molecular dynamics simulations.</span></p>
MD simulation of POPC lipids bilayer at 310K (Berger, Gromacs 3.1.4)
<p>Simulation data and files for POPC Berger simulation at 310K used in publication J. Phys. Chem. B 2007, 111, 3139-3150.</p>
MD simulation trajectory of SDPE/CHOL bilayer and related files
<p>Simulation trajectory pre-equiblirated SDPE/CHOL bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2021.2 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 86 SDPE, 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/CHOL bilayer and related files
<p>Simulation trajectory pre-equiblirated POPE/CHOL bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2021.2 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 86 POPE, 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 (18.75 mol%) bilayer and related files
<p>Simulation trajectory pre-equiblirated POPE/DOG bilayer and related files from all-atom molecular dynamics simulations. The system contains 18.75mol% DOG. Simulations have been performed with GROMACS-2021.2 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 104 POPE, 24 DOG 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 data for a pure DOPC bilayer (1000 mM CaCl2) with AMOEBA force field + OpenMM
<p>MD simulation data for the DOPC bilayer + 1000 mM CaCl2 with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 DOPC lipids, 36 CaCl2 ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
MD Simulation data for a pure DOPC bilayer (450 mM NaCl) with AMOEBA force field + OpenMM
<p>MD simulation data for the DOPC bilayer + 450 mM NaCl with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 DOPC lipids, 17 NaCl ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
MD Simulation data for a pure DOPC bilayer (450 mM CaCl2) with AMOEBA force field + OpenMM
<p>MD simulation data for the DOPC bilayer + 450 mM CaCl2 with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 DOPC lipids, 16 CaCl2 ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
MD Simulation data for a pure DOPC bilayer (1000 mM NaCl) with AMOEBA force field + OpenMM
<p>MD simulation data for the DOPC bilayer + 1000 mM NaCl with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 DOPC lipids, 35 NaCl ions, and 2880 water molecules. The trajectory is 201,61 ns long (20161 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Comparison of methods for bulk automated simulation of glycosidic bond conformations - MD trajectory data
<p>MD trajectories (supplementary data for the article)</p>
MD Simulation movies 1,2,3
<p>MD Simulation movies 1,2,3</p>
MD Simulation Carcinoma Antigen [Replicates-Data]
<p><strong>MD-simulation data files </strong><br><strong>ACC1:</strong> Saquamous cell carcinoma antigen [replicate 1]<br><strong>ACC2:</strong> Saquamous cell carcinoma antigen [replicate 2]<br><strong>HMGB1:</strong> Hemoglobin [replicate 1]<br><strong>HMGB2:</strong> Hemoglobin [replicate 2]<br><strong>PSA1:</strong> Prostate specific antigen [replicate 1]<br><strong>PSA2:</strong> Prostate specific antigen [replicate 2]</p> <p><strong>RMSD:</strong> Root mean square deviation<br><strong>RMSF:</strong> Root mean square fluctuation</p>
MD Simulation Data
<p>MD Simulation Data has been provided to check the reproducibility of the results</p>
parameter and coordinate files to start an MD simulation of Haloferax volcanii ADH2
<p>parameter and coordinate files to start an MD simulation of Haloferax volcanii ADH2 in Amber</p>
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OpenNeuro
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