Molecular Dynamics trajectories and portable binary run input (TPR) files for the dual role of anionic lipids in amyloid aggregation

About this repository

We conducted Coarse-Grained molecular dynamics simulations to study the aggregation of the amyloid-beta fragment, Aβ16-22 (K16LVFFAE22), on mixed lipid bilayers composed of POPC and POPS. Three bilayer compositions were examined: 0% PS-100% PC, 10% PS-90% PC and 30% PS-70% PC. Simulations were performed using GROMACS 2019.4, employing the WEPROM forcefield for peptide modeling and WEPMEM for lipid modeling. For each POPS percentage, four independent replicas were run for 3000 ns. 

Contents

> Abeta_PCPS.zip 

This zip file contains three main folders: 0PS, 10PS, and 30PS. These represent different percentages of PS present in the lipid bilayer.

Each folder contains:

1. Initial structures:   - em1.gro: Lipid bilayer without peptides   - eq1.gro: Lipid bilayer at 95 Ų area-per-lipid (APL)   - em2.gro: Lipid bilayer at 95 Ų APL with 16 peptides   - eq2.gro: Final equilibrated structure with peptides (used for production)

2. Supporting files:   - index.ndx: Index groups for peptides and lipid bilayer   - run.pdf: Structure file for VMD visualization

3. Four replica folders (replica1 to replica4), each containing:   - red.tpr: Binary input for analysis (peptides and lipid bilayer only)   - full_trj_pbc.xtc: Trajectory file (peptides and lipid bilayer only, centered in box)

Note: The `.tpr` files were created using the `gmx convert-tpr` tool.

To access the source files with which these simulations were set-up, and a brief tutorial, see: https://github.com/meenaljainumd/PCPS_amyloid_aggregation