The foundation model (FM) paradigm is transforming Machine Learning Force Fields (MLFFs), leveraging general-purpose representations and scalable training to perform a variety of computational chemistry tasks. Although MLFF FMs have begun to close the accuracy gap relative to first-principles methods, there is still a strong need for faster inference speed. Additionally, while research is increasingly focused on general-purpose models which transfer across chemical space, practitioners typically only study a small subset of systems at a given time. At test time, MLFFs must also obey physical constraints unique to the downstream use case, such as energy conservation for molecular dynamics simulations. This underscores the need for fast, specialized MLFFs relevant to specific downstream applications, which preserve test-time physical soundness while maintaining train-time scalability. In this work, we introduce a method for transferring general-purpose representations from MLFF foundation models to smaller, faster MLFFs specialized to specific regions of chemical space. We formulate our approach as an architecture-agnostic knowledge distillation procedure, where the smaller "student" MLFF is trained to match the Hessians of the energy predictions of the "teacher" foundation model. We demonstrate our approach across multiple recent foundation models, large-scale datasets, chemical subsets, and downstream tasks. Our specialized MLFFs can be up to 20 times faster than the original foundation model, while retaining, and in some cases exceeding, its performance and that of undistilled models. We also show that distilling from a teacher model with a direct force parameterization into a student model trained with conservative forces (i.e., computed as derivatives of the potential energy) successfully leverages the representations from the large-scale teacher for improved accuracy, while maintaining energy conservation during test-time molecular dynamics simulations. More broadly, our work suggests a new paradigm for MLFF development, in which foundation models are released along with smaller, specialized simulation ``engines" for common chemical subsets. The implementation of our method is available at https://github.com/ASK-Berkeley/MLFF-distill.

Transition path sampling (TPS), which involves finding probable paths connecting two points on an energy landscape, remains a challenge due to the complexity of real-world atomistic systems. Current machine learning approaches rely on expensive training procedures and under-utilize growing quantities of atomistic data, limiting scalability and generalization. Generative models of atomistic conformational ensembles sample temporally independent states from energy landscapes, but their application to TPS remains mostly unexplored. In this work, we address TPS by interpreting candidate paths as trajectories sampled from stochastic dynamics induced by the learned score function of generative models, namely denoising diffusion and flow matching. Under these dynamics, finding high-likelihood transition paths becomes equivalent to minimizing the Onsager-Machlup (OM) action functional, enabling us to repurpose pre-trained generative models for TPS in a zero-shot fashion. We demonstrate our approach on a Müller-Brown potential and several fast-folding proteins, where we obtain diverse, physically realistic transition pathways, as well as tetrapeptides, where we demonstrate successful TPS on systems not seen by the generative model during training. Our method can be easily incorporated into new generative models, making it practically relevant as models continue to scale and improve.