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Cited by 6Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsComputational Drug Discovery Methods

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Visualizing the energy landscape for a molecular dynamics trajectory

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Neuman, Vilmos, Wesołowski, Patryk A., Bojarski, Krzysztof K., Dewan, Diksha, Schäffler, Moritz, Smardz, Pamela, Wales, David J.·2026·The Journal of Chemical Physics
DOI 10.1063/5.0310206

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Abstract

We introduce an open-source program that converts molecular dynamics trajectories into disconnectivity graphs, providing a concise and interpretable visualization of the energy landscape that has been traversed. Our approach applies Savitzky–Golay smoothing to per-frame thermodynamic traces (potential energy in NVE/NVT or enthalpy in NPT 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 optimization. The method is ensemble-agnostic and compatible with both all-atom and coarse-grained simulations. For some representative biochemical systems, it processes 104–105 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 for a selected energy and time resolution, offering an interpretable structural summary of conformational hierarchies with minimal postprocessing. Because extrema are detected directly from the trajectory, the graphs reflect the organization of the explored region of the landscape on the molecular dynamics timescale. Our approach basically substitutes local minima and maxima from the smoothed time series as proxies for the true stationary points of the underlying landscape.

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Metadata

Authors
Neuman, V., Wesołowski, P. A., Bojarski, K. K., Dewan, D., Schäffler, M., Smardz, P., & Wales, D. J.
Affiliations
  • University of Cambridge (GB)
  • Gdańsk University of Technology (PL)
  • Forschungszentrum Jülich (DE)
  • Institute of Physics (PL)
ORCID
Venue
The Journal of Chemical Physics
Publisher
AIP Publishing
Published
2026-01-23
Volume
164
Issue
4
ISSN
  • 0021-9606 (ISSN-L)
  • 1089-7690
DOI
10.1063/5.0310206
OpenAlex
W7125515831
Cited by
6
References
3
Citations by year
2026: 6
FWCI
12.55
Type
journal article
Language
en
Open access
Licence
Locations
  • The Journal of Chemical Physics (publishedVersion, cc-by)
  • ChemRxiv (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Apollo (cc-by)
Funders
  • Travel Grant of St Hilda’s College, University of Oxford
  • Cambridge and Oxford Alumni Club of Hungary Scholarship
  • Gates Cambridge Trust
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Keywords
energy landscape, disconnectivity graphs, molecular dynamics trajectories, Savitzky-Golay filter, transition state, conformational space, coarse-grained simulation, open source software, landscape topology

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