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299 results for “MD simulation”
MD simulation trajectory of SDG/SDPE bilayer and related files
<p>Raw simulation trajectory data of pre-equiblirated SDG/SDPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.6 with Lipid17 force field and TIP3P water model. The trajectory is 0-2100 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 12 SDG, 116 SDPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p>
MD simulation trajectory of SDG/POPE bilayer and related files
<p>Raw simulation trajectory data of pre-equiblirated SDG/POPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.6 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-2100 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 12 SDG, 116 POPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p>
Water, acetonitrile, and methanol MD simulations driven by many-body ML potentials
<p>Input, output, and trajectories of molecular dynamics (MD) simulations of water, acetonitrile, and methanol. Simulations were driven by many-body machine learning (mbML) potentials including explicit 1-, 2-, and 3-body contributions. <a href="https://keithgroup.github.io/mbGDML/">GDML</a>, <a href="https://libatoms.github.io/GAP/">GAP</a>, and <a href="https://schnetpack.readthedocs.io/en/stable/">SchNet</a> models are provided in a <a href="https://doi.org/10.5281/zenodo.7112163">separate repository</a>. All simulations were performed in the <a href="https://wiki.fysik.dtu.dk/ase/">atomic simulation environment (ASE)</a>. Analyses including radial distribution function (rdf) curves are provided <a href="https://github.com/keithgroup/mbgdml-h2o-meoh-mecn">here</a>.</p> <p><strong>Manifest</strong></p> <p>The following simulations are included in this repository for each solvent.</p> <ul> <li>1 ps hexamer NVE MD simulation driven by MP2/def2-TZVP (in ORCA v4.2.0), mbGDML, mbGAP, mbSchNet, and GFN2-xTB started with the same positions and velocities. Velocities were initialized at 298.15 K with a Maxwell-Boltzmann distribution.</li> <li>Periodic NVT MD simulation at 298.15 K for 10 or 30 ps with a 1 fs time step driven by mbGDML. These simulations contained <ul> <li>58 or <strong>137</strong> water molecules,</li> <li><strong>67</strong> or 122 acetonitrile molecules,</li> <li><strong>61</strong> methanol molecules.</li> </ul> </li> </ul> <p>Systems that are not bolded were used for testing purposes.</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 715mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 715 mM CaCl2 (104 POPC, 24 POPS, 26 POPS, 4306 WAT, 72 Ca2+, 112 Cl-). Additional Ca2+ cations added to neutralize the negative charge of POPS (leading to total Ca2+ concentration of 919 mM). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 300 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC bilayer with 716mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC bilayer with 716 mM CaCl2 (128 POPC, 26 POPS, 4308 WAT, 56 Ca2+, 112 Cl-). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 200 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 102mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 102 mM CaCl2 (104 POPC, 24 POPS, 26 POPS, 4306 WAT, 24 Ca2+, 16 Cl-). Additional Ca2+ cations added to neutralize the negative charge of POPS (leading to total Ca2+ concentration of 306 mM). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 300 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC bilayer with 100mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC bilayer with 100 mM CaCl2 (128 POPC, 26 POPS, 4452 WAT, 8 Ca2+, 16 Cl-). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 200 ns trajectories were calculated with the last 100 ns stored here).</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
Molecular Dynamics (MD) Simulation Data for Dynamics Underlie the Drug Recognition Mechanism by the Efflux Transporter EmrE
<p>MD simulations on the proton bound (PDB 8UWU), deprotonated on E14A (PDB 8UWU), TPP Bound (PDB 8UWU) on our NMR derived structures.</p> <p> </p> <p>MD simulations on the proton bound (7MH6) and deprotonated on E14A (7MH6) on X-ray structures. </p> <p> </p> <p>Total raw simulation data would be too large for uploading to repositories. To reduce size of file, starting structure and tpr files are uploaded. Final structure at 2.5 μs are also uploaded. </p>
3D-coordinates of the complex formed by TRN-1 and CA hexamer from HIV-1 and MD simulation of H27 with CA hexamer
<p>The complex formed by HIV-1 CA hexamer (based on 3H4E) and Transportin-1 (TRN-1, based on 4FQ3) was first obtained by rigid docking and optimized by MD simulations and finally energy minimized using NAMD program and Charmm36m force field. This complex was used for the in silico screening study for discovering new antiviral drugs.</p> <p>The 3D coordinates (PDB file) of CA hexamer in presence of H27</p> <p>The corresponding trajectory of MD simulation (500 ns) of H27 with CA hexamer in order to find preferential binding sites (trajectory reduced or strided for reducing the size of the file</p>
Nucleosome core particle MD simulations
<p>Gromacs topology files and xtc trajectory files of nucleosome core particule containing the alpha-palindromic sequence based on the 1KX5 PDB structure with 0.15 M of NaCl salt. Each trajectory is of 1 µs. Force field used: Amber14ff with IDP correction for the histone tails, parmbsc1, TIP3P water model.</p> <p>The letter in the name of the file are associated to a given simulation (1kx5-a_sol.top is related to 1kx5_sol-a.xtc).</p>
Files for MD simulation of adsorption of amino acids onto the PVC surface
<p>Input files, parameter files and forcefield parameters for 50 ns MD simulation of AA acid adsorption onto the PVC surface.</p>
MD simulations data for Hirschi et al. (2024)
<p>This repository contains the initial coordinates and final output coordinate files for Molecular Dynamics (MD) simulations. The data is organized and named according to the following convention:</p> <ul> <li><strong>PDB ID of Seeding Structure</strong>: Identifier of the protein structure used to initiate the simulation.</li> <li><strong>Type of Ligand</strong>: Indicates the presence and type of ligand bound to the protein. <ul> <li><code>schiff</code>: Retinal forming a Schiff base</li> <li><code>dka</code>: Decanoate</li> <li><code>apo</code>: No ligand</li> </ul> </li> <li><strong>Replica Number</strong>: Number assigned to each independent simulation run (1, 2, or 3).</li> <li><strong>Simulation Stage</strong>: Indicates whether the file corresponds to the initial structure (<code>0</code>) or the final frame of the simulation (<code>final</code>).</li> </ul> <h4>Example File Names:</h4> <ul> <li><code>7B03_apo_3_final.pdb</code>: Final frame of the third replica simulation of the apo state of the protein with PDB ID 7B03.</li> <li><code>7B03_schiff_1_0.pdb</code>: Initial structure of the first replica simulation with a Schiff base ligand for the protein with PDB ID 7B03.</li> </ul> <h4>Simulation Details:</h4> <ul> <li><strong>Replica 1</strong>: A long simulation with a duration of 950 nanoseconds (ns).</li> <li><strong>Replicas 2 and 3</strong>: Two shorter simulations, each lasting 400 ns.</li> </ul>
MD simulation trajectory of cannabidiol in the cannabinoid type 1 receptor
<p>MD simulation trajectory of cannabidiol in the presence of an orthosteric THC and Rimonabant in the CB1R active and inactive conformations respectively. The protein–ligand complexes were inserted in a POPC lipid bilayer and solvated in a TIP3 water box with Na+ and Cl- ions. Simulations were run with NAMD 2.9 software using periodic boundary conditions and Particle Mesh Ewald (PME) for long-range electrostatics. Total production time for the inactive and active receptor conformations were 25 ns and 50 ns respectively.<br> </p>
MD simulation data: Intrinsic disorder is a conserved feature of hepatitis C virus E2 glycoprotein
<p><strong>Background</strong></p> <p>Equilibration, relaxation and production runs were performed on GPUs using the CUDA version of PMEMD in AMBER 16 and AMBER ff14SB force field. Minimisation steps were performed on a CPU using PMEMD in AMBER 16 and the AMBER ff14SB force field. The GLYCAM_06j-1 force field was used for the simulations of the glycosylated E2. All software is available from http://ambermd.org/. </p> <p><strong>Contents</strong></p> <p>There are three tarball (<strong>.tar.gz</strong>) files, one for each of the HCV strain investigated. </p> <p>The contents of each tarball is as follows:</p> <p>1. a source PDB (<strong>.pdb</strong>) file</p> <p>2. <strong>leap.scr</strong> - a script used to create the .prmtop and .inpcrd files</p> <p>3. Two AMBER parameter/topology (<strong>.prmtop</strong>) (one with hydrogen mass repartitioning) and an AMBER coordinate (<strong>.inpcrd</strong>) file </p> <p>4. Multiple control (<strong>.ctl</strong>) files numbered 1 to 10 that are used to minimize (<strong>min</strong> prefix), relax (<strong>rel</strong> prefix) and equilibrate (<strong>equ</strong> prefix) the model</p> <p>5. Executable <strong>do_md</strong> that performed all the minimisation, relaxation and equilibration steps</p> <p>6. File <strong>parmed.txt</strong> used to repartition the hydrogen atom mass (for the unglycosylated simulations)</p> <p>7. control file <strong>prod.ctl</strong> used for the production run </p> <p>8. Executable <strong>run_prod</strong> that was used to perform the production run</p> <p>9. Two control files (<strong>prod_short.ctl </strong>and <strong>prod_short_2.ctl</strong>) for the short runs used to de-correlate the simulation for the independent runs</p> <p>10. Executable <strong>run_short</strong> and <strong>run_short_2</strong> used to carry out the de-correlated production runs.</p> <p>10. Five AMBER trajectory (<strong>.nc</strong>) files for five independent MD simulations, numbered 1 to 5. <strong>Note: </strong>each of these files is over 2GB.</p>
MD simulations files for: Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning
<div>Colvar files and related python scripts of Ala2 and Ala10 simulations.</div>
MD Simulation Files for Dual BACH1 regulation by complementary SCF-type E3 ligases
<p>MD Simulation input files and analysis files for the SKP1-FBXO22/BACH1<sup>BTB</sup> complex, SKP1-FBXO22 by itself, BACH1<sup>BTB</sup>, and the BACH1<sup>BTB</sup> F9A mutant.</p>
The P-V-T dataset of liquid Fe-C alloys from FP-MD simulations
<p>The <em>P</em>-<em>V</em>-<em>T</em> dataset of liquid Fe-C 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.</p>
Data file containing MD simulation data
<p>Data file containing MD simulation data in Schrodinger maestro readable format and MMGBSA data in microsoft excel file</p> <p> </p> <p> </p>
Progeny Project Gromacs MD Simulations of the MW8 surfactant
<p>"MW8" thiophene based surfactant molecule at the water-vacuum interface, data from the PROGENY project ,<br> gromacs 2021.2 input and output.<br> From the trajectories contained in this archive density profiles and surface tensions can be extracted.</p> <p>Different number of molecules per surface in each sub directory. See README.txt.</p>
MD simulation video about a h-BN growth on Pt(111) surface
<p>Videos of a h-BN growth on a Pt(111) surface. This simulation is performed by a machine learning potential. The deposit ratio of B and N atoms is 1:3. The B and N atoms are deposited on the Pt(111) surface. Total MD time is 20 ns. (500B,1500N)-Pt(111).1300to1300K.0to3ns.mp4 file is the MD simulation trajectory during 0 to 3 ns. (500B,1500N)-Pt(111).1300to900K.10to12ns.mp4 file is the MD simulation trajectory during 10 to 12 ns. </p>
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