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299 results for “MD simulation”
MD simulation trajectory of SDPE/DOG/CHOL bilayer and related files
<p>Simulation trajectory pre-equiblirated SDPE/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 SDPE, 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>
Dataset wih MD simulations of fish aquaporin - wt and different mutants.
<p>MD trajectories and final minimized structures after 100 ns MD simulation for wt, pT38, pY107, L117A, Y107A and Y107E variants of fish aquaporin.</p> <p>All simulations performed using the YASARA software (www.yasara.org). </p>
RNA-FUS MD simulation ensembles
<p>Amber parm files MD simulation <strong>S</strong> ensembles in .xtc format. Water molecules are stripped and only each one ns is stored. Data from Pokorna et al.: Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations, 2022.</p>
Dataset: Polystyrene and SARS-CoV-2 S protein MD simulations
<p>Coordinates (input files and equilibrated structures) corresponding to the MD simulations reported in Sahihi and Faraudo, J. Chem. Inf. Model. 2022, 62, 16, 3814–3824 <a href="https://doi.org/10.1021/acs.jcim.2c00562">https://doi.org/10.1021/acs.jcim.2c00562</a> . Please cite this publication and the dataset in any use of the data.</p> <p>The coordinate files in pdb format include fully glycosylated structures of the S1 subunit of SARS-CoV-2 spike protein (up and down confirmations) and a polystyrene slab.</p>
MD Simulation data, results and scripts for "Simulating the Skin Permeation Process of Ionizable Molecules"
<p>Input and output data from MD simulations in the "Simulating the Skin Permeation Process of Ionizable Molecules" article.</p> <p>The data of the uncharged permeants were already published in Lundborg et al. <br>Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates. Biophys. J. 2022, 121, 3837-3849.</p> <p>Also includes scripts to rerun the analyses.</p>
MD simulations associated to the paper "A PDZ tandem repeat folds and unfolds via different pathways"
<p>These are the MD simulation data generated for this study. The files are:</p> <p>x11_plain_simulation: training data, charmm22*+tip3p simulation of X11 PD1-PDZ2</p> <p>x11_random_coil: reference random coil data for X11 PDZ1-PDZ2</p> <p>x11_e0.21_0.335_folding_t310: 200 folding simulations</p> <p>x11_e0.21_0.335_melting_t380: 200 unfolding simulations</p> <p>x11d2_e0.21_0.33_folding_t310: 200 folding simulations for the isolated PDZ2</p> <p>x11_e0.21_0.33_folding_t310_d2open: 200 folding simulations for X11 PDZ1-PDZ2 starting with PDZ1 folded and the C-ter tail bound</p>
MD simulation trajectories for paper "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms"
<div> <div>The dataset includes the MD simulation trajectories for the paper "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms". </div> <div>Citation: Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Mol Cell. 2021 Jan 7;81(1):166-182.e6. PMID: 33238161; PMCID: PMC7796963.</div> </div>
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>
Movies from MD simulations of oxygen permeation in a POPC bilayer with and without cholesterol
<p>Movies from MD simulations of oxygen permeation in a POPC bilayer with and without cholesterol.</p> <p> </p> <p> </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>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip3p, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip3p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip4p, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip4p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, OPC4, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, OPC4 water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip3p, 303K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip3p water model at 303K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p> <p> </p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip4p, 303K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip4p water model at 303K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip4p, 298K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip4p water model at 298K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, OPC4, 310K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, OPC4 water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip4p, 310K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip4p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip3p, 298K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip3p water model at 298K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
CHARMM36 POPC/POPE (50%-50%) MD simulation (300 K - 300ns - 1 bar)
<p>CHARMM36 POPC 50% POPE 50% bilayer simulation (300 K, starting structure from CHARMM-GUI with 128 POPC and 128 POPE lipids (64 per leaflet for each species) fully hydrated with 34 water molecules per lipid). The trajectory contains the whole simulation from 0 to 300 ns skipped every 100 ps and centered on the P atoms. No ions were added as there is no charge in the system. This bilayer was used to calculate the order parameter and the area per lipid for the NMRlipids project (on the time window 50-300 ns).</p> <p> </p>
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