Trajectory data generated by a virtual-system coupled canonical molecular dynamics simulation with a coarse-grained model of glutamine-octapeptide dimer.

The trajectory data of the coarse-grained molecular dynamics simulation with the glutamine-octapeptide dimer generated by myPresto/omegagene. The details of simulation is reported in the manuscript "myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling" (doi: 10.2142/biophysico.BSJ-2020013) The file "md.trr" is recorded in GROMACS .trr format, which can be visualized by using some standard molecular viewers such as VMD (https://www.ks.uiuc.edu/Research/vmd/) We recommend visualize the trajectory by using "VDW" or "points" representations for "Drawing Method". The methods depending on connectivity information, e.g., "NewCartoon" and "lines", are not working because of coarse graining. This file included the 10,000 snapshots analyzed in the "Example" section of the manuscript. As described in the manuscript, 10 independent runs of 10^7 steps of simulation were done as production runs. The snapshots were recorded at every 10,000 steps, and 1,000 snapshots were recorded for each run. The "md.trr" file was generated by concatenating these snapshots over 10 runs. The file "q8dimer.pdb" is the initial coordinates of the simulation model. Each atom represents a bead corresponding to one amino acid residue. The cell-dimension of cubic periodic boundary cell is 60 Å.本数据集为通过myPresto/omegagene生成的谷氨酰胺八肽二聚体（glutamine-octapeptide dimer）粗粒度分子动力学模拟（coarse-grained molecular dynamics simulation）轨迹数据。相关模拟细节已发表于论文《myPresto/omegagene 2020：面向虚拟系统耦合采样的分子动力学模拟引擎》（DOI: 10.2142/biophysico.BSJ-2020013）。 文件"md.trr"采用GROMACS的.trr格式存储，可通过VMD（https://www.ks.uiuc.edu/Research/vmd/）等标准分子可视化工具进行可视化。我们推荐采用"VDW"或"points"作为绘图方法展示轨迹；由于采用粗粒度建模，依赖连接信息的绘图方式（如"NewCartoon"和"lines"）无法正常使用。该文件包含了论文"示例"章节中分析的10000帧轨迹快照。 如论文所述，本次生产模拟共开展10次独立运行，每次运行包含10^7步模拟过程。每10000步记录一帧轨迹快照，因此每次运行可采集1000帧快照。最终的"md.trr"文件即为将10次运行的所有轨迹快照拼接整合得到的。 文件"q8dimer.pdb"为模拟体系的初始坐标文件，其中每个粗粒度粒子（bead）对应一个氨基酸残基。体系采用立方周期性边界单元，晶胞尺寸为60 Å（埃）。