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Molecular dynamics (MD) simulations allow the exploration of the phase spaceof biopolymers through the integration of equations of motion of theirconstituent atoms. The analysis of MD trajectories often relies on the choiceof collective variables (CVs) along which the dynamics of the system isprojected. We developed a graphical user interface (GUI) for facilitating theinteractive choice of the appropriate CVs. The GUI allows: defininginteractively new CVs; partitioning the configurations into microstatescharacterized by similar values of the CVs; calculating the free energies ofthe microstates for both unbiased and biased (metadynamics) simulations;clustering the microstates in kinetic basins; visualizing the free energylandscape as a function of a subset of the CVs used for the analysis. A simplemouse click allows one to quickly inspect structures corresponding to specificpoints in the landscape.

METAGUI 3: a graphical user interface for choosing the collective variables in molecular dynamics simulations