Title: METAGUI 3: a graphical user interface for choosing the collective variables in molecular dynamics simulations,
Abstract: Molecular dynamics (MD) simulations allow the exploration of the phase space
of biopolymers through the integration of equations of motion of their
constituent atoms. The analysis of MD trajectories often relies on the choice
of collective variables (CVs) along which the dynamics of the system is
projected. We developed a graphical user interface (GUI) for facilitating the
interactive choice of the appropriate CVs. The GUI allows: defining
interactively new CVs; partitioning the configurations into microstates
characterized by similar values of the CVs; calculating the free energies of
the microstates for both unbiased and biased (metadynamics) simulations;
clustering the microstates in kinetic basins; visualizing the free energy
landscape as a function of a subset of the CVs used for the analysis. A simple
mouse click allows one to quickly inspect structures corresponding to specific
points in the landscape.