Dataset for Molecular Dynamics Simulation of TLR4/MD-2 Complex with β-Sesquiphellandrene

Dataset Overview This dataset contains the input and processed molecular dynamics (MD) simulation data supporting the computational findings of our study. The simulations modeled the interaction between the TLR4/MD-2 receptor complex and the lead bioactive ligand β-sesquiphellandrene from Aframomum Melegueta over a 100-nanosecond trajectory. --- Associated Project: "Integrated In Vivo and In Silico Analysis Reveals Aframomum Melegueta Neuroprotection Against LPS-Induced Memory Impairment Through TLR4/MD-2 Modulation" License: Creative Commons Attribution 4.0 International (CC-BY 4.0) --- File Inventory & Description Simulation Inputs (Topology & Structure)* complex_solvated.gro`: The final solvated system coordinates (Protein + Ligand + Water + Ions).* topol.top: GROMACS system topology file.* ligand.itp: Ligand topology parameters generated via CGenFF.* index.ndx: Index file defining groups (System, Protein, Ligand, Solvent).* md_input files: .edr, .nvt, .npt, .cpt, .gro files, etc. Production Outputs* md_01 xtc file: Compressed trajectory file (100 ns simulation, frames saved every 10 ps).* md_01 tpr file: The run input file used to generate the trajectory.* md_01 log file: GROMACS log file containing energy and performance data. Analysis Outputs (Processed Data)* rmsd.xvg, rmsf.xvg, potential.xvg, --- Methodology Summary Software: GROMACS (Version 2025.2)Force Field: CHARMM36m (Protein) / CGenFF (Ligand)Water Model: TIP3PEnsemble: NPT (Isothermal-Isobaric)Temperature: 300 K (V-rescale thermostat)Pressure: 1 bar (Parrinello-Rahman barostat)Duration: 100 nsTime Step: 2 fs --- Citation If you use this dataset, please cite both the dataset DOI and the associated publication: Dataset: Oladele, T. S., Iteire, K. A., Ogunmiluyi, O. E., Adebisi, K. A., Siyanbade, A. J., Sulaiman, K. A., Leko, B. J., & Ijomone, O. M. (2026). Dataset for Molecular Dynamics Simulation of TLR4/MD-2 Complex with β-Sesquiphellandrene (v1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18468770