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

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. Program summary Program Title: {METAGUI} 3 Program Files doi: http://dx.doi.org/10.17632/wyxjndwkbp.1 Licensing provisions: {GPLv3} Programming language: Tcl/Tk, Fortran Journal reference of previous version: {METAGUI} [1] Does the new version supersede the previous version?: No Nature of problem: Choose the appropriate collective variables for describing the thermodynamics and kinetics of a biomolecular system through biased and unbiased molecular dynamics. Solution method: Provide an environment to compute and visualize free energy surfaces as a function of collective variables, interactively defined. Additional comments: {METAGUI} 3 is not a standalone program but a plugin that provides analysis features within {VMD} (version 1.9.2 or higher). o [[1]] X. Biarn?s, F. Pietrucci, F. Marinelli, A. Laio, METAGUI. A {VMD} interface for analyzing metadynamics and molecular dynamics simulations, Computer Physics Communications 183 (2012) 203-211.