Published applications of PyRETIS

This collection highlights peer-reviewed applications of PyRETIS across molecular kinetics, condensed-phase chemistry, biomolecular transitions, and method development. Each study couples a physical system with a path-sampling strategy and an associated publication.

Where available, Source files lead to runnable inputs: a retis.rst for PyRETIS 3, the corresponding retis.toml for PyRETIS 4, and a README describing requirements and execution. Large solvated and ab initio systems are intended for HPC environments and require system-specific convergence studies.

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Biomolecular kinetics

ABL-imatinib kinetics with RETIS and REPPTIS.

RETIS and REPPTIS were used to characterise the ABL-imatinib transition at atomistic resolution, assessing path-sampling performance and rare-event kinetic estimates in a large biomolecular system.

Source files Package to be recovered and mirrored.

Publication W. Vervust, D. T. Zhang, E. Riccardi, T. S. van Erp and A. Ghysels, Path sampling challenges in large biomolecular systems: RETIS and REPPTIS for ABL-imatinib kinetics, Biophys. J. 124, 3932-3947 (2025).

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Method development

Memory reduction using partial path ensembles.

Partial path ensembles and replica exchange were examined as a route to reduce path-storage requirements when long-lived metastable states govern the reaction dynamics.

Source files Repository

Publication W. Vervust, D. T. Zhang, T. S. van Erp and A. Ghysels, Path sampling with memory reduction and replica exchange to reach long permeation timescales, Biophys. J. 122, 2960-2972 (2023).

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Condensed-phase dynamics

Rupture of a thin liquid film.

Wire Fencing and Stone Skipping subtrajectory Monte Carlo moves were applied to dodecane-film rupture in water with GROMACS, providing a condensed-phase benchmark for enhanced path sampling.

Source files Download inputs

Publication D. T. Zhang, E. Riccardi and T. S. van Erp, Enhanced path sampling using subtrajectory Monte Carlo moves, J. Chem. Phys. 158, 024113 (2023).

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Ab initio kinetics

Redox reaction of a diruthenium complex.

The subtrajectory moves were evaluated for an ab initio CP2K model of a diruthenium aqua complex, where the high cost of each force evaluation makes efficient path generation essential.

Source files Download inputs

Publication D. T. Zhang, E. Riccardi and T. S. van Erp, Enhanced path sampling using subtrajectory Monte Carlo moves, J. Chem. Phys. 158, 024113 (2023).

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Data-driven analysis

ChemiTrees for reaction-path interpretation.

Decision-tree analysis was used as a post-processing workflow for path-sampling trajectories of proton exchange in formic acid-water clusters, identifying geometric descriptors that distinguish reactive and unreactive paths.

Source files Package to be recovered and mirrored.

Publication S. Roet, C. D. Daub and E. Riccardi, Chemistrees: data driven identification of reaction pathways via machine learning, J. Chem. Theory Comput. 17, 6193-6202 (2021).

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Proton-transfer dynamics

Proton transfer in a water trimer.

Proton transfer in a polarizable water trimer provides a compact reference system for examining path-sampling trajectories and the analysis and visualisation workflows in PyVisA.

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Publication O. Aarøen, H. Kiær and E. Riccardi, PyVisA: Visualization and Analysis of path sampling trajectories, J. Comput. Chem. 42, 435-446 (2021).

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Atmospheric chemistry

Formic acid catalysed formation of sulfuric acid.

The formic-acid-catalysed conversion of sulfur trioxide and water to sulfuric acid was investigated to resolve competing mechanisms and determine their temperature-dependent rate constants.

Source files Download inputs

Publication C. D. Daub, E. Riccardi, V. Hänninen and L. Halonen, Path sampling for atmospheric reactions: formic acid catalysed conversion of SO3 + H2O to H2SO4, PeerJ Phys. Chem. 2, e7 (2020).

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Biomolecular recognition

Predicting the mechanism and rate of H-NS binding to AT-rich DNA.

H-NS adsorption to AT-rich DNA was studied at atomistic resolution with GROMACS. Metadynamics identified metastable basins, and RETIS was used to calculate transition pathways and kinetic rates.

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Publication E. Riccardi, E. C. van Mastbergen, W. W. Navarre and J. Vreede, Predicting the mechanism and rate of H-NS binding to AT-rich DNA, PLoS Comput. Biol. 15, e1006845 (2019).

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Aqueous reaction dynamics

Autoionization of water.

Born–Oppenheimer DFT simulations combined with RETIS were used to resolve water autoionization pathways and quantify their kinetics. Machine-learning analysis assessed the discriminatory power of the candidate order parameters.

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Publication M. Moqadam, A. Lervik, E. Riccardi, V. Venkatraman, B. K. Alsberg and T. S. van Erp, Local initiation conditions for water autoionization, Proc. Natl. Acad. Sci. U.S.A. 115, E4569-E4576 (2018).

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Protein conformational dynamics

Conformational study of Cyclophilin - A.

Atomistic GROMACS simulations were used to sample structural rearrangements of cyclophilin A and estimate their transition rates.

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Publication Manuscript in preparation.