Our recent developments in graph theory algorithms applied to molecular dynamics trajectories (DFT-based and classical MD) are presented. 1 – Graph theory for the automatic recognition of 3D conformers along MD trajectories, at the atomistic granularity level, isomorphism being a key component together with keeping the atoms chemical nature. Isomorphism allows recognize conformations and provides graphs of transitions, the reduction in the isomorphism complexity has been achieved by the introduction of “orbits” and “reference snapshots.” The method provides the changes in conformations over time based on hydrogen bond(s), proton transfer(s), coordination number(s), covalent bond(s), fragmentation(s). We will show applications to gas phase molecules and clusters as well as direct transferability to condensed matter. 2 – Graph theory and deep learning for going from the graphs to 3D molecular structures, showing applications to peptides of increasing complexity. 3 – Graph theory for the assignment of anharmonic vibrational modes from MD simulations, building one graph/vibrational mode, without harmonic approximations. Graph vertices are made of the internal coordinates self-contributions to the mode while the graph edges contain the correlations between the internal coordinates. All coupling motions are therefore naturally included in the graph modes. The ultimate advantage of graphs is the capability for comparing graphs and extracting similarities, exactly what is needed for comparing vibrational modes between molecular systems, and this will be illustrated for peptides and their dimers. 4 – Gas phase polymers are highly flexible hence displaying complex dynamics, which analysis in terms of time-evolution of the 3D structures is rather complicated. We have developed graphs algorithms to analyze such trajectories directly in terms of the polymorphism of the H-Bonded rings over time. Illustrations will be given on Z-Ala6 and Gramicidin peptides, to emphasize that this graph level granularity is the only one giving rise to a comprehensive view of the 3D structures time-evolution.

Graph theory for molecular dynamics simulations

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.