Visual Interactive Analysis of Molecular Dynamics Simulation

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Today, classical force field Molecular Dynamics (MD) simulations are routinely carried out in full atomistic detail for systems involving several million atoms over time scales ranging into the microsecond region and it has become an indispensable tool in the field of materials and life sciences. Those simulations are generating a wealth of data that must be analyzed, which is currently done with a multitude of decoupled tools for visualizing trajectories and extracting statistical data making an interactive exploration infeasible. Events of interest however are hidden in long time series and complex geometric structures. Therefore an interactive approach is fundamental for exploring the data and understanding the key geometrical parameters at play. For the last two years we have developed a visual environment for exploration of simulated molecules and their descriptive properties. The environment is built on tight integration of statistics, plots and visualization of the molecules. In this talk, I will illustrate how this tool has been used to explore interactively dataset connected to both material and life sciences, as for instance with the case of a biomarker used to detect amyloid fibril misfold related to Alzheimer’s disease.