Umbrella sampling data of AuNP interacting with a PC bilayer

Files in Gromacs (v4.6) format used to generate the PMF profile shown in Fig. 3 in [1]. The nanoparticle is pulled to the EC leaflet in the 'genstart' simulations. The initial structures for the umbrella sampling windows are extracted from this trajectory. The files obtained from umbrella sampling windows are named 'pullX.*', where X is the distance between the centers of mass of the AuNP and the EC leaflet phosphori. Trajectories (.xtc) are saved every 100ps. Additionally, the initial and final structures (.gro), the run input files (.tpr), energy files (.edr), log files (.log), checkpoint files (.cpt), simulation parameter files (.mdp), and the files generated by the pull code (pull forces and pull distances, .xvg) are given for each umbrella window. Additionally, an index file (index.ndx) and a topology file (topol.top) common for all systems is provided. TOP.tar contains the molecule definitions (.itp). 'pullf-files.dat' and 'tpr-files.dat' are used by g_wham to extract the profile shown in Fig. 3 (except for the choice of the zero level) by 'g_wham -it tpr-files.dat -if pullf-files.dat -b 40000 -nBootstrap 100' [1] Heikkilä et al., Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations, J. Phys. Chem. C, 2014, 118 (20), pp 11131–11141, DOI: 10.1021/jp5024026本数据集包含用于生成文献[1]中图3所示平均力势（Potential of Mean Force, PMF）剖面的Gromacs（v4.6）格式文件。在'genstart'模拟任务中，纳米粒子被拉向胞外侧小叶层（Extracellular leaflet, EC）。伞形采样（umbrella sampling）窗口的初始结构均从该模拟轨迹中提取。从各伞形采样窗口获取的文件命名为'pullX.*'，其中X代表金纳米颗粒（Gold Nanoparticle, AuNP）与EC小叶层磷原子的质心间距。轨迹文件（.xtc）每100皮秒保存一次。此外，每个伞形采样窗口均配套提供初始与最终结构文件（.gro）、运行输入文件（.tpr）、能量文件（.edr）、日志文件（.log）、检查点文件（.cpt）、模拟参数文件（.mdp），以及由pull代码生成的包含拉力与拉距数据的.xvg格式文件。同时，还提供了所有体系通用的索引文件（index.ndx）与拓扑文件（topol.top）。TOP.tar压缩包内含分子定义文件（.itp）。`pullf-files.dat`与`tpr-files.dat`可通过g_wham工具提取得到图3所示的剖面（零能级选择除外），具体执行命令为：`g_wham -it tpr-files.dat -if pullf-files.dat -b 40000 -nBootstrap 100`。[1] Heikkilä 等. 阳离子型金纳米颗粒与质膜样脂质双层的结合：原子模拟揭示的自发细胞渗透潜在机制. 《The Journal of Physical Chemistry C》, 2014, 118(20): 11131–11141, DOI: 10.1021/jp5024026

搜集汇总

背景与挑战

背景概述

该数据集包含金纳米颗粒（AuNP）与磷脂酰胆碱（PC）双层膜相互作用的伞形采样模拟数据，采用Gromacs（v4.6）格式，用于生成平均力势（PMF）剖面图以研究纳米颗粒自发渗透细胞的潜在机制。数据集包括初始结构、多个伞形采样窗口的轨迹文件（.xtc）、能量文件（.edr）、输入文件（.tpr）等，总大小约11.4 GB，覆盖从距离6到50的多个采样点，并提供相关索引和拓扑文件以支持后续分析。