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

Abstract

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