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关于本存储库 本研究通过粗粒度分子动力学模拟（Coarse-Grained molecular dynamics simulations），探究了淀粉样β肽片段Aβ16-22（K16LVFFAE22）在由1-棕榈酰-2-油酰-sn-甘油-3-磷酸胆碱（POPC）与1-棕榈酰-2-油酰-sn-甘油-3-磷酸丝氨酸（POPS）构成的混合脂质双分子层表面的聚集行为。本次研究共设置三种脂质双分子层组分：0% PS-100% PC、10% PS-90% PC与30% PS-70% PC。模拟采用GROMACS 2019.4软件完成，肽链建模使用WEPROM分子力场，脂质建模使用WEPMEM分子力场。针对每一种POPS占比，均运行4组独立重复模拟，模拟时长为3000纳秒（ns）。 内容说明 > Abeta_PCPS.zip 该压缩包包含三个核心文件夹：0PS、10PS与30PS，分别对应脂质双分子层中不同的POPS占比。 每个文件夹均包含以下内容： 1. 初始结构文件： - em1.gro：不含肽链的脂质双分子层结构文件 - eq1.gro：单脂质分子面积（area-per-lipid, APL）为95 Ų的脂质双分子层结构文件 - em2.gro：单脂质分子面积为95 Ų且包含16条肽链的脂质双分子层结构文件 - eq2.gro：包含肽链的最终平衡结构文件（用于生产模拟） 2. 辅助文件： - index.ndx：用于划分肽链与脂质双分子层的索引组文件 - run.pdf：用于VMD可视化的结构文件 3. 四个重复模拟文件夹（replica1至replica4），每个文件夹内包含： - red.tpr：仅用于肽链与脂质双分子层分析的二进制输入文件 - full_trj_pbc.xtc：仅包含肽链与脂质双分子层的轨迹文件（已在模拟盒中居中对齐） 注：所有.tpr文件均通过`gmx convert-tpr`工具生成。 如需获取本模拟的构建源文件与简要教程，请访问：https://github.com/meenaljainumd/PCPS_amyloid_aggregation