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

## TL;DR

METAGUI 3 is an interactive graphical tool that simplifies the selection, analysis, and visualization of collective variables in molecular dynamics simulations, enhancing understanding of biopolymer behavior.

## Contribution

It introduces a user-friendly GUI for defining CVs, microstate partitioning, free energy calculation, clustering, and visualization in MD analysis.

## Key findings

- Facilitates interactive CV selection and microstate analysis.
- Enables quick visualization of free energy landscapes.
- Supports both unbiased and biased MD 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.