# FlashSchNet: Fast and Accurate Coarse-Grained Neural Network Molecular Dynamics

arXiv: https://arxiv.org/abs/2602.13140 · HTML: https://mlsanity.com/paper/2602.13140/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 43 references that are in the map.
- First posted on arXiv 13 Feb 2026.

## Builds on (most cited first, 18 of 18)

- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges](https://mlsanity.com/paper/2104.13478/) (2021)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields](https://mlsanity.com/paper/2206.07697/) (2022)
- [Optimal Brain Compression: A Framework for Accurate Post-Training Quantization and Pruning](https://mlsanity.com/paper/2208.11580/) (2022)
- [Learning Local Equivariant Representations for Large-Scale Atomistic Dynamics](https://mlsanity.com/paper/2204.05249/) (2022)
- [Orb: A Fast, Scalable Neural Network Potential](https://mlsanity.com/paper/2410.22570/) (2024)
- [GNNAdvisor: An Adaptive and Efficient Runtime System for GNN Acceleration on GPUs](https://mlsanity.com/paper/2006.06608/) (2020)
- [GE-SpMM: General-purpose Sparse Matrix-Matrix Multiplication on GPUs for Graph Neural Networks](https://mlsanity.com/paper/2007.03179/) (2020)
- [Machine Learning Coarse-Grained Potentials of Protein Thermodynamics](https://mlsanity.com/paper/2212.07492/) (2022)
- [FusedMM: A Unified SDDMM-SpMM Kernel for Graph Embedding and Graph Neural Networks](https://mlsanity.com/paper/2011.06391/) (2020)
- [Navigating protein landscapes with a machine-learned transferable coarse-grained model](https://mlsanity.com/paper/2310.18278/) (2023)
- [TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations](https://mlsanity.com/paper/2402.17660/) (2024)
- [DF-GNN: Dynamic Fusion Framework for Attention Graph Neural Networks on GPUs](https://mlsanity.com/paper/2411.16127/) (2024)

## Abstract (arXiv)

Graph neural network (GNN) potentials such as SchNet improve the accuracy and transferability of molecular dynamics (MD) simulation by learning many-body interactions, but remain slower than classical force fields due to fragmented kernels and memory-bound pipelines that underutilize GPUs. We show that a missing principle is making GNN-MD IO-aware, carefully accounting for reads and writes between GPU high-bandwidth memory (HBM) and on-chip SRAM. We present FlashSchNet, an efficient and accurate IO-aware SchNet-style GNN-MD framework built on four techniques: (1) flash radial basis, which fuses pairwise distance computation, Gaussian basis expansion, and cosine envelope into a single tiled pass, computing each distance once and reusing it across all basis functions; (2) flash message passing, which fuses cutoff, neighbor gather, filter multiplication, and reduction to avoid materializing edge tensors in HBM; (3) flash aggregation, which reformulates scatter-add via CSR segment reduce, reducing atomic writes by a factor of feature dimension and enabling contention-free accumulation in both forward and backward passes; (4) channel-wise 16-bit quantization that exploits the low per-channel dynamic range in SchNet MLP weights to further improve throughput with negligible accuracy loss. On a single NVIDIA RTX PRO 6000, FlashSchNet achieves 1000 ns/day aggregate simulation throughput over 64 parallel replicas on coarse-grained (CG) protein containing 269 beads (6.5x faster than CGSchNet baseline with 80% reduction of peak memory), surpassing classical force fields (e.g. MARTINI) while retaining SchNet-level accuracy and transferability.