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393 results for “Molecular dynamics simulations”
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 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>
Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations
<p>MD trajectories of SL1, SL2, SL2+SL3, SL4, and SL5a elements in SARS-CoV-2 5'UTR</p>
Data related to the article "Molecular dynamics simulations for the prediction of thermophysical properties of plutonium-based molten salts"
<p>Contains input files and data used to generate the figures of the article:</p> <p>Molecular dynamics simulations for the prediction of thermophysical properties of plutonium-based molten salts<br>(Giovanni Pireddu*, Mirella Simoes Santos*, David Lambertin, Timothée Kooyman)<br><br>*:Equal contribution</p> <p>Journal of Nuclear Materials<br>DOI: https://doi.org/10.1016/j.jnucmat.2024.155124</p> <p>The folder EXAMPLE_INPUT_FILES contains typical MetalWalls(https://doi.org/10.21105/joss.02373) (repository(https://gitlab.com/ampere2/metalwalls)) input files used to perform the molecular simulations.</p> <p>The folder DATA_FIGURES contains the processed data used to plot the figures of the paper (see below).</p> <p><br>Figure 2:<br>- 'Fig2_Density.dat' : density as a function of temperature (binary system, calculated from MD simulations)</p> <p>Figure 3:<br>- 'Fig3_HCap.dat' : heat capacity as a function of temperature (binary system, calculated from MD simulations)</p> <p>Figure 4:<br>- 'Fig4_Density.dat' : density as a function of temperature (ternary system, calculated from MD simulations)</p>
Trajectory of DYRK1A-Q17 Complex from 200-ns Molecular Dynamics Simulation
Open the record for dataset details and reuse information.
Molecular Dynamics simulation data for the article "Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism"
<p>Zipped archives with MD simulation data for the article "Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism" (eLife, accepted).</p>
Molecular dynamics simulation of human ρ1 GABAA receptor with neurosteriod THDOC
<p>Molecular dynamics simulation trajectory, parameter files for the systems of human ρ1 GABAA receptor with neurosteriod TDHOC.</p>
Molecular dynamics simulation of human ρ1 GABAA receptor with neurosteriod pregnanolone
<p>Molecular dynamics simulation trajectory, parameter files for the systems of human ρ1 GABAA receptor with neurosteriod pregnanolone.</p>
Molecular dynamics simulation of rat EDAA TRPV2 with drugs
<p>Molecular dynamics simulation trajectory, parameter files for the systems of rat EDAA TRPV2 with drugs.</p>
Molecular dynamics simulation dataset
<p>This dataset contains Molecular Dynamics trajectories of 9 endecapeptides, positioned in the pore construct. One trajectory is done in absence of any transolcating peptide.</p> <p>.xtc files correspond to the trajectories and the .gro files contain the corresponding structures, they can be viewed, for example, with VMD.</p> <p>Every trajectory is the concatenation of 8 trajectories, of 125 ns each, which differ for the orientation of the centrai side-chain with respect to the frame of the pore. The following name parts indicate the central residue. The 73-80 files correspond to the construct alone, taken as a reference. </p> <p>1-8 trp; 9-16 tyr; 17-24 arg; 25-32 his; 33-40 glu; 41-48 gln; 49-56 ser; 57-64 ile; 65-72 gly; 73-80 no peptide.</p>
Molecular Dynamics simulations (filtered small system)
<p><span>Molecular Dynamics of E. coli ribosomes stalled by the nascent peptide SecM(Ms).</span></p> <p><span>Four systems were simulated: Control, K, N and WT.<span> </span></span></p> <p><span>To facilitate analysis, each system was filtered to include all the residues within 15 Angstroms of the </span><span>nascent chain, including the nascent chain, and the complete tRNA. The resulting structure is shared as a </span><span>pdb file with suffix "within15_tunnel.pdb"</span></p> <p><span>For each system, 5x50 ns trajectories were simulated. </span><span>And the concatenated trajectory is shared (suffix: "within15_concatenated.xtc")</span></p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (A47V) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (A47V).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (G46S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (G46S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (F55L) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (F55L).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (F39L) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (F39L).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (D59Y) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (D59Y).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (E76G) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (E76G).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of rat phenylalanine hydroxylase (rPAH) tetramer
<p>Raw data of molecular dynamics simulations of rat phenylalanine hydroxylase (T22-K450) tetramer. Missing residues were rebuilt using Modeller. Metal site was parameterized using MCPB.py in AmberTools. Simulation starts from the crystal pose (PDB: 5DEN).</p>
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International Brain Laboratory public data
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OpenNeuro
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