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.

本数据集收录了由myPresto/omegagene生成的谷氨酰胺-八肽二聚体的粗粒化分子动力学模拟轨迹。该模拟的详细信息已报道于论文《myPresto/omegagene 2020：一种用于虚拟系统耦合采样的分子动力学模拟引擎》（doi: 10.2142/biophysico.BSJ-2020013）中。文件“md.trr”采用GROMACS .trr格式记录，可通过诸如VMD（https://www.ks.uiuc.edu/Research/vmd/）等标准分子查看器进行可视化。建议使用“VDW”或“points”表示法进行轨迹绘制，而依赖连接信息的方法，例如“NewCartoon”和“lines”，由于粗粒化处理而无法使用。此文件包含了论文“示例”部分分析的10,000个快照。正如论文所述，进行了10次独立的、每步数为10^7的模拟作为生产运行，每10,000步记录一次快照，每次运行记录1,000个快照。这些快照通过10次运行拼接生成“md.trr”文件。文件“q8dimer.pdb”包含模拟模型的初始坐标，其中每个原子代表一个对应于单个氨基酸残基的球体。立方周期性边界单元的细胞维度为60埃。