Molecular Dynamics Simulations of Aβ40–Aβ42 Co-aggregates in PBS and CSF Conditions

This dataset contains the molecular dynamics (MD) input, parameter, and trajectory files for two systems simulating the co-aggregation of amyloid-beta 40 (Aβ40) and amyloid-beta 42 (Aβ42) peptides on a gold nanosheet surface in physiologically relevant environments. The Aβ42 fibril is modelled as a 24-mer, and the Aβ40 oligomer as a 9-mer docked onto the fibril using ZDOCK. Simulations were performed under two conditions: phosphate-buffered saline (PBS) and cerebrospinal fluid (CSF), each with the corresponding ionic composition and concentration. All simulations were conducted using GROMACS 2020.6 with the CHARMM36m force field (July 2021 release). The complete force field directory (charmm36-jul2021.ff/) is included to ensure reproducibility. Simulations were run for 300 ns each, with all coordinates, topologies, and parameter files provided. Systems Provided (2 total) 1. Aβ40–Aβ42 co-aggregate in PBSFolder: PBS/Contains: coaggregate_pbs.pdb – initial peptide complex structure. topol_pbs.top – full system topology. .itp and posre.itp files – individual include and position restraint files for all 9 Aβ40 chains and 24 Aβ42 chains. coaggregate_pbs.gro – minimized, solvated and ionised configuration. coaggregate_pbs.xtc – MD trajectory (300 ns). charmm36-jul2021.ff/ – complete CHARMM36m force field directory. 2. Aβ40–Aβ42 co-aggregate in CSFFolder: CSF/Contains: coaggregate_csf.pdb – initial peptide complex structure. topol_csf.top – full system topology. .itp and posre.itp files – individual include and position restraint files for all 9 Aβ40 chains and 24 Aβ42 chains. coaggregate_csf.gro – minimized, solvated and ionised configuration. coaggregate_csf.xtc – MD trajectory (300 ns). charmm36-jul2021.ff/ – complete CHARMM36m force field directory. File Description .pdb – Initial peptide complex structure on gold nanosheet. .top – System topology referencing all molecular components. .itp – Include files for individual peptides and restraints. .gro – Coordinates of solvated and ionised system after minimization. .xtc – Compressed MD trajectory (300 ns). charmm36-jul2021.ff/ – Force field parameters for reproducibility. All files are provided to allow full reproducibility of the simulations and enable further analysis of Aβ40–Aβ42 co-aggregation under different ionic environments.