TIMELINE: TRAJECTORY ANALYSIS AND EVENT IDENTIFICATION IN VMD

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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 importantevents. This traditionally requires a scientist to spend many hours reviewing animatedstructures, examining different regions of a large simulated system, andcalculating appropriate geometric, statistical, and other properties. A more productiveuse of a scientist's time is to use a "whole-trajectory" view, produced byperforming analysis calculations for every frame of a trajectory, and for each smallcomponent of the entire simulated structure  for example, calculating the secondarystructure of every residue of a protein, and for every frame of a trajectory. The 2Dplot that results allows quick identification of events that take place throughout thetrajectory. With the move to petascale computation, such analysis is increasinglynecessary: as system sizes, time scales, and trajectory counts grow, the time requiredto manually review animated structures becomes impractical, while the timerequired to asses a static whole-trajectory plot remains the same.