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691 results for “Molecular dynamics”
Figure 2 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 2 Benchmarking docking binding energy scores distribution: (a) AutoDock, (b) AutoDock Vina.
Molecular Mechanism of Substrate Transport and Dynamics of the Cyanobacterial Bicarbonate Transporter BicA
<p>Molecular Mechanism of Substrate Transport and Dynamics of the Cyanobacterial Bicarbonate Transporter BicA</p>
Raw data molecular dynamics and alphafold (Lemaire et al)
<p>Raw data molecular dynamics and alphafold for manuscript NCOMMS-24-29370</p>
Molecular Dynamics Assessment of Primary Damage Efficiency for Fusion Relevant Elements Dataset
<p>Dataset containing simulation results and example input scripts for the paper "Molecular Dynamics Assessment of Primary Damage Efficiency for Fusion Relevant Elements".</p>
Immersion enthalpies of nanomaterials (metals, metal oxides, organic chemistry structures) in water and octanol through molecular dynamics simulations with GROMACS and LAMMPS software
<p>Molecular dynamics simulations (free energy calculations) of water interface properties of spherical and Wulff structures nanoparticles (metals, metal oxides and carbon structures) with GROMACS and LAMMPS software.</p>
Molecular Dynamics trajectories and portable binary run input (TPR) files for the dual role of anionic lipids in amyloid aggregation
<h1>About this repository</h1> <p>We conducted Coarse-Grained molecular dynamics simulations to study the aggregation of the amyloid-beta fragment, Aβ16-22 (K16LVFFAE22), on mixed lipid bilayers composed of POPC and POPS. Three bilayer compositions were examined: 0% PS-100% PC, 10% PS-90% PC and 30% PS-70% PC. Simulations were performed using GROMACS 2019.4, employing the WEPROM forcefield for peptide modeling and WEPMEM for lipid modeling. For each POPS percentage, four independent replicas were run for 3000 ns. </p> <h1><strong>Contents</strong></h1> <h3>> Abeta_PCPS.zip </h3> <p>This zip file contains three main folders: 0PS, 10PS, and 30PS. These represent different percentages of PS present in the lipid bilayer.</p> <p>Each folder contains:</p> <p>1. Initial structures:<br> - em1.gro: Lipid bilayer without peptides<br> - eq1.gro: Lipid bilayer at 95 Ų area-per-lipid (APL)<br> - em2.gro: Lipid bilayer at 95 Ų APL with 16 peptides<br> - eq2.gro: Final equilibrated structure with peptides (used for production)</p> <p>2. Supporting files:<br> - index.ndx: Index groups for peptides and lipid bilayer<br> - run.pdf: Structure file for VMD visualization</p> <p>3. Four replica folders (replica1 to replica4), each containing:<br> - red.tpr: Binary input for analysis (peptides and lipid bilayer only)<br> - full_trj_pbc.xtc: Trajectory file (peptides and lipid bilayer only, centered in box)</p> <p>Note: The `.tpr` files were created using the `gmx convert-tpr` tool.</p> <p><strong>To access the source files with which these simulations were set-up, and a brief tutorial, see: </strong><a href="https://github.com/suhasgotla/heparin_amyloid_self-assembly">https://github.com/meenaljainumd/PCPS_amyloid_aggregation</a></p>
Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of tetraglyme-LiTFSI liquid electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 1.00 e/nm².</p> <p>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of polymer chain length on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of monoglyme-LiTFSI liquid electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 1.00 e/nm².</p> <p>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations Confined Between Charged Electrodes With Various Surface Charges: Plots
<p>Plots of the data contained in the data sets</p> <ul> <li>Uncharged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13164944">https://doi.org/10.5281/zenodo.13164944</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165450">https://doi.org/10.5281/zenodo.13165450</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165725">https://doi.org/10.5281/zenodo.13165725</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13166024">https://doi.org/10.5281/zenodo.13166024</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> </ul> </li> <li>Charged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13166152">https://doi.org/10.5281/zenodo.13166152</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167128">https://doi.org/10.5281/zenodo.13167128</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167338">https://doi.org/10.5281/zenodo.13167338</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167551">https://doi.org/10.5281/zenodo.13167551</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167614">https://doi.org/10.5281/zenodo.13167614</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes With Various Surface Charges</li> </ul> </li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes With Various Surface Charges
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of polymer chain length and electrode surface charge on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 0.25 e/nm², +/- 0.50 e/nm² and +/- 0.75 e/nm². Data for surface charges of +/- 0.00 e/nm² and +/- 1.00 e/nm² are contained in <a href="https://doi.org/10.5281/zenodo.13164944">https://doi.org/10.5281/zenodo.13164944</a> and <a href="https://doi.org/10.5281/zenodo.13166152">https://doi.org/10.5281/zenodo.13166152</a>, respectively.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes (+/- 1.00 e/nm²)
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of polymer chain length on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 1.00 e/nm².</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of monoglyme-LiTFSI liquid electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of tetraglyme-LiTFSI liquid electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 1.00 e/nm².</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Trajectories for GPR6 with Ligand S1P
<p>Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling</p> <p>Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
sulphate and molybdate incorporation at calcite-water interface - ab initio molecular dynamics data
<p>Provided here are ab initio molecular dynamics data files generated in CP2K, relating to the publication entitled<br> Sulphate and Molybdate Incorporation at the Calcite-Water Interface: Insights from Ab Initio Molecular Dynamics. By Scott D. Midgley, Devis Di Tommaso, Dominik Fleitmann, Ricardo Grau-Crespo.</p> <p>We have provided the CP2K input file (.inp), the CP2K energy file (.ener), and a single geometry snapshot from the simulation (.xyz).<br> It is not possible to share the fully dynamics trajectory, because each file is extremely large.</p> <p>N.B. for the sulphate ion in water, a corruption in the .ener file meant that it was not possible to share. Instead a list of MD energies are given as a .txt file, with energies in eV.<br> </p>
Molecular dynamic simulation data of liquid Al-Cu alloys
<p>This dataset contains all obtained data for molecular dynamics investigation of Al-Cu melts.</p>
Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore: Molecular dynamics simulation data
<p>Atomistic molecular dynamics simulation data set accompanying manuscript "Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore".</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.