TIMELINE: TRAJECTORY ANALYSIS AND EVENT IDENTIFICATION IN VMD

University Of Illinois At Urbana-Champaign, Urbana IL

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Abstract

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 [unreadable]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.