109 Molecular dynamics done quick: efficient trajectory analysis software

Abstract

Molecular dynamics (MD) simulation nowadays is an essential part of biological, chemical, and physical research. There is a vast variety of accurate and high-performance MD software facilitating the task. However, simulations of biopolymers on meaningful time scales always produce large trajectories rarely amenable to manual analysis. Such analysis, and especially meaningful data search and extraction, often becomes a bottleneck of in silico experiment along with actual MD computations. Most of the existing software for analysis of MD simulation results is based on command-line, script-guided processes that require the researchers to have an idea about programming language constructions used, often applied to the one and only product, providing an excessive set of analytic features, but sacrificing ease of use, simplicity, and clarity. In this work, we present an open source, cross-platform, GUI-based program, Molecular Dynamics Trajectory Reader and Analyzer (MDTRA), which may be helpful in addressing such issues. MDTRA is a versatile program and does not require scripting (yet supports it), is able to quickly plot the analysis results, and minimizes RAM requirements (Popov et al., 2012). A key MDTRA feature is the logical organization of data handling and treatment. Our program introduces a convenient way to manage data based on a principle of a re-useable “conveyor”, which delivers results from “streams” (trajectories) through “data sources” to “result collectors.” Each stage is adjustable at any time, causing only the affected data sources to be rebuilt. MDTRA allows users to plot and analyze distances, angles, and forces in the molecule. It also implements trajectory-related search and extraction tools, including determination of meaningful torsions of protein backbone, search for stable hydrogen bonds, building 2D-RMSD diagrams, and massive comparative plotting of DNA parameters. MDTRA proved itself useful in a study of DNA repair enzymes OGG1, Fpg, and MutY. An example of analysis of the mobility of tryptophan residues contributing to fluorescence of E. coli Fpg (observed experimentally by Kuznetsov et al., 2007) is shown in the figure.