Molecular Dynamics Simulation of Amyloid-β and α-Synuclein in solution

This repository contains all-atom molecular dynamics simulation data and analysis code for the study of early co-aggregation between amyloid-β42 (Aβ42) and α-synuclein (α-syn) in aqueous solution. Three systems were simulated, each in five independent 3 µs replicates (45 µs total): α-syn with (1) a single Aβ42 monomer, (2) two independent Aβ42 monomers, and (3) an Aβ42 monomer together with a pre-formed Aβ42 dimer. Simulations were run in GROMACS 2023.2 with the CHARMM36m force field. The deposit includes the production trajectories (water and ions stripped, PBC-corrected), the topologies and run inputs, the full set of GROMACS input files needed to reproduce the simulations, and the analysis scripts used in the associated manuscript (aggregation events, intermolecular contact maps, temporal contact coordination, β-hairpin analysis, structural-ensemble comparison, configurational entropy, and convergence diagnostics). See the README for the folder layout and instructions.