Benchmarks

Kernel benchmarks

Local:

python scripts/benchmark_kernel.py --sub-frames 250

Docker reproduction: see docker/README.md in the repository.

Reference (4-CPU Docker, 3 replicates × 250 frames, 2,722 atoms each):

Method	Total time (s)	Rust speedup
Rust	0.047	1.00×
MDTraj	0.803	17.19×
MDA	1.126	24.12×