A new loss function based on the application of It\={o}'s formula is proposed to learn the committor function with a minimization procedure on the parameters of a neural network to better approximate the committor function using a better sampling of the reactive trajectories.
Abstract
Many molecular dynamics simulations aim at studying transitions between two states (from reactants to products). In this context, the committor function (which gives for a given molecular configuration the probability to reach the product state before the reactant state) is a pivotal quantity, in particular because it is the optimal importance function for rare event simulation methods such as importance sampling or splitting techniques. These methods are used to sample the reactive path ensemble, and estimate for example the transition rate. However, learning such a function is generally a challenging task due to the high dimensionality of the configuration space. In this work, after reviewing the existing methodologies to construct approximate committor functions, a new loss function based on the application of It\={o}'s formula is proposed to learn the committor function with a minimization procedure on the parameters of a neural network. After comparing this novel approach to existing procedures on the M\"uller--Brown potential, we introduce a coupling strategy with the Adaptive Multilevel Splitting method to better approximate the committor function using a better sampling of the reactive trajectories. This methodology in which the committor function is iteratively learned only requires initially the knowledge of the reactant and product states.
MARC-TS, a two-stage framework that learns a continuous, endpoint-conditioned path, queries it at any resolution and uses local path context to refine a transition-state candidate, is introduced.
Most molecular transitions occur on timescales far beyond direct molecular dynamics simulations. The committor, the probability that a configuration reaches a product state before a reactant state, is a central kinetic statistic, providing a mechanism-independent reaction coordinate and a foundation for transition path...
General-purpose machine-learning interatomic potentials (MLIPs) for organic reactions need to be accurate on both the minimum energy path (MEP) for static evaluation of basic properties and the broader configurational space for simulating reaction dynamics. Existing general datasets for gas-phase organic reactions rely...
Wan-Run Jiang, Jin-Zhe Zeng, Man-Yi Yang et al.· 0 citations
The committor is the optimal reaction coordinate for a rare transition: it pinpoints the transition state and fixes the rate, and it governs events from protein folding to crystal nucleation. It minimises a Dirichlet energy, whose value at the minimum is the reactive flux, over functions that vanish on the reactant sta...
M. Petersen, Simon M. Lichtinger, Roberto Covino· 0 citations
GenAIMMD is introduced, an iterative algorithm that actively and self-consistently learns the ideal reaction coordinate (the committor) and trains a conditioned Boltzmann Generator to sample from arbitrary bias windows along it, providing a correlation-free and fully parallelizable path sampling scheme that does not re...
Maximilian Negedly, Sebastian Falkner, A. Coretti et al.· 0 citations
Transition-state searches remain a major bottleneck in reaction discovery, as identifying valid saddle-point structures requires numerous expensive quantum-chemical calculations. Generative models can reduce this burden by proposing candidates from reactant and product geometries, but supervised training on geometries...
Yun-Yang Li, Ze-Chang Sun, Kuang Yu et al.· 0 citations
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