Visualising the Energy Landscape for a Molecular Dynamics Trajectory

We introduce an open-source program that converts molecular dynamics trajectories into disconnectivity graphs, providing a concise and interpretable visualisation of the energy landscape that has been traversed. Our approach applies Savitzky–Golay smoothing to per-frame thermodynamic traces (potential energy in N V E/N V T or enthalpy in N P T ensembles), to identify local extrema as proxies for minima and transition states, and generates the necessary files for disconnectivity graph construction. This workflow requires no additional geometry optimisation. The method is ensemble-agnostic and compatible with both all-atom and coarse-grained simulations. For some representative biochemical systems, it processes 10000–100000 frames in seconds on a standard laptop and produces an approximate representation of the underlying landscape topology. The resulting graphs capture the structures that are visited and pathways between them only for a selected energy and time resolution, offering an interpretable structural summary of conformational hierarchies with minimal preprocessing. Because extrema are detected directly from the trajectory, the graphs reflect the organisation of the explored region of the landscape on the molecular dynamics time scale. Our approach basically substitutes local minima and maxima from the smoothed time series as proxies for the true stationary points of the underlying landscape.