Making Room for AI: Multi-GPU Molecular Dynamics with Deep Potentials in GROMACS

GROMACS is a de-facto standard for classical Molecular Dynamics (MD). The rise of AI-driven interatomic potentials that pursue near-quantum accuracy at MD throughput now poses a significant challenge: embedding neural-network inference into multi-GPU simulations retaining high-performance. In this work, we integrate the MLIP framework DeePMD-kit into GROMACS, enabling domain-decomposed, GPU-accelerated inference across multi-node systems. We extend the GROMACS NNPot interface with a DeePMD backend, and we introduce a domain decomposition layer decoupled from the main simulation. The inference is executed concurrently on all processes, with two MPI collectives used each step to broadcast coordinates and to aggregate and redistribute forces. We train an in-house DPA-1 model (1.6 M parameters) on a dataset of solvated protein fragments. We validate the implementation on a small protein system, then we benchmark the GROMACS-DeePMD integration with a 15,668 atom protein on NVIDIA A100 and AMD MI250x GPUs up to 32 devices. Strong-scaling efficiency reaches 66% at 16 devices and 40% at 32; weak-scaling efficiency is 80% to 16 devices and reaches 48% (MI250x) and 40% (A100) at 32 devices. Profiling with the ROCm System profiler shows that >90% of the wall time is spent in DeePMD inference, while MPI collectives contribute <10%, primarily since they act as a global synchronization point. The principal bottlenecks are the irreducible ghost-atom cost set by the cutoff radius, confirmed by a simple throughput model, and load imbalance across ranks. These results demonstrate that production MD with near ab initio fidelity is feasible at scale in GROMACS.

Discovering Governing Equations of Geomagnetic Storm Dynamics with Symbolic Regression

Geomagnetic storms are large-scale disturbances of the Earth's magnetosphere driven by solar wind interactions, posing significant risks to space-based and ground-based infrastructure. The Disturbance Storm Time (Dst) index quantifies geomagnetic storm intensity by measuring global magnetic field variations. This study applies symbolic regression to derive data-driven equations describing the temporal evolution of the Dst index. We use historical data from the NASA OMNIweb database, including solar wind density, bulk velocity, convective electric field, dynamic pressure, and magnetic pressure. The PySR framework, an evolutionary algorithm-based symbolic regression library, is used to identify mathematical expressions linking dDst/dt to key solar wind. The resulting models include a hierarchy of complexity levels and enable a comparison with well-established empirical models such as the Burton-McPherron-Russell and O'Brien-McPherron models. The best-performing symbolic regression models demonstrate superior accuracy in most cases, particularly during moderate geomagnetic storms, while maintaining physical interpretability. Performance evaluation on historical storm events includes the 2003 Halloween Storm, the 2015 St. Patrick's Day Storm, and a 2017 moderate storm. The results provide interpretable, closed-form expressions that capture nonlinear dependencies and thresholding effects in Dst evolution.

Automatic Particle Trajectory Classification in Plasma Simulations

Numerical simulations of plasma flows are crucial for advancing our understanding of microscopic processes that drive the global plasma dynamics in fusion devices, space, and astrophysical systems. Identifying and classifying particle trajectories allows us to determine specific on-going acceleration mechanisms, shedding light on essential plasma processes. Our overall goal is to provide a general workflow for exploring particle trajectory space and automatically classifying particle trajectories from plasma simulations in an unsupervised manner. We combine pre-processing techniques, such as Fast Fourier Transform (FFT), with Machine Learning methods, such as Principal Component Analysis (PCA), k-means clustering algorithms, and silhouette analysis. We demonstrate our workflow by classifying electron trajectories during magnetic reconnection problem. Our method successfully recovers existing results from previous literature without a priori knowledge of the underlying system. Our workflow can be applied to analyzing particle trajectories in different phenomena, from magnetic reconnection, shocks to magnetospheric flows. The workflow has no dependence on any physics model and can identify particle trajectories and acceleration mechanisms that were not detected before.