TIMELINE: TRAJECTORY ANALYSIS AND EVENT IDENTIFICATION IN VMD

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 分析MD弹道的过程的一个关键部分是识别重要的 事件。传统上，这需要科学家花费许多小时来审查动画 结构，检查大型模拟系统的不同区域，以及 计算适当的几何、统计和其他属性。工作效率更高 利用科学家的时间就是使用由以下方法产生的“全轨迹”观点 对轨迹的每一帧和每一小块执行分析计算 组件的整个模拟结构，例如，计算次 蛋白质的每一个残基的结构，以及轨迹的每一帧。二维图 通过绘制结果图，可以快速识别在整个 弹道。随着向PB级计算的转变，这样的分析越来越多 必要：随着系统规模、时间范围和轨迹计数的增长，所需时间 手动查看动画结构变得不切实际，而时间 评估静态全轨迹图所需的时间保持不变。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. A key part of the process of analyzing an MD trajectory is identifying important events. This traditionally requires a scientist to spend many hours reviewing animated structures, examining different regions of a large simulated system, and calculating appropriate geometric, statistical, and other properties. A more productive use of a scientist's time is to use a "whole-trajectory" view, produced by performing analysis calculations for every frame of a trajectory, and for each small component of the entire simulated structure  for example, calculating the secondary structure of every residue of a protein, and for every frame of a trajectory. The 2D plot that results allows quick identification of events that take place throughout the trajectory. With the move to petascale computation, such analysis is increasingly necessary: as system sizes, time scales, and trajectory counts grow, the time required to manually review animated structures becomes impractical, while the time required to assess a static whole-trajectory plot remains the same.