Molecular Dynamics Simulations of Amyloid-β Peptides and Cu(II) Complex at a Biomimetic Water/Dichloroethane Interface

This dataset contains the molecular dynamics (MD) input, parameter, and trajectory files for three systems: 1. Aβ₁₋₁₆ at the water/DCE interface with all counterions and tetrabutylborate (TB⁻)2. Aβ₄₋₁₆ at the water/DCE interface with all counterions and TB⁻3. Aβ₄₋₁₆–Cu(II) complex at the water/DCE interface with all counterions and TB⁻ The simulations were conducted using GROMACS 2020.6 with the CHARMM36m force field, modified to include parameters for the organic anion TB⁻ (BATB) and cation BA+ (BTPPA) and other counterions, as well as the DCE organic phase. All peptide systems were simulated at pH 5 using appropriate protonation states. Systems Provided (3 total) Aβ₁₋₁₆ at the water/DCE interface (with TB⁻) Folder: Abeta_1_16 Contains structure (ab_1_16.pdb), full force field parameters (charmm36m_added.ff/), topology (topol.top), minimized configuration (min_nopbc.gro), trajectory (md_dt200.xtc), and position restraints (posre.itp). Aβ₄₋₁₆ at the water/DCE interface (with TB⁻) Folder: Abeta_4_16 Contains structure (ab_4_16.pdb), same charmm36m force field, and corresponding .top, .gro, .xtc, and .itp files. Aβ₄₋₁₆–Cu(II) complex at the water/DCE interface (with TB⁻) Folder: Abeta_4_16_Cu Includes ab_4_16_cu.pdb with the Cu(II)-coordinated peptide, the modified force field, full system topology, and trajectory. Each system includes the full charmm36m_added.ff/ directory to ensure reproducibility. This contains .itp and .gro files for water models, organic ions, and all non-bonded and bonded parameters used. All structure, parameter, and trajectory files are provided to ensure full reproducibility. File Description .pdb Initial peptide structure with protonation states .top Topology file referencing all force field components .itp Include files for molecule definitions and restraints .gro Coordinates of solvated systems after minimization .xtc MD trajectory files (100 ns) charmm36m_added.ff/ Complete force field directory with added DCE and organic ion parameters