MDAnalysis2.9.0 + waterdynamics1.2.0 + PathSimAnalysis1.2.1
20 real TIP3P waters,201 consecutive frames0..20ps after native unwrap+sequentialNoJump.
51 real ubiquitin frames,76 C-alpha atoms aligned to one common reference. Reverse path is an algebraic ordering control, not another MD trajectory.
./setup.sh
./run.sh
./verify.sh
./plot.sh
Outputs:results/FULL-FIELDS.npz,results/VALIDATION.json,plots/*.png.
No relaxation time, diffusion coefficient, free energy, or path kinetic convergence is claimed. Slab residence uses laboratory z on continuous coordinates. WOR/MSD origin spacing follows native lag stride.
Private local .deps install only; shared software untouched. Wheels retain upstream licenses and metadata. Numeric native histogram values are used instead of rounded graph text; Frechet class paths explicitly use double arithmetic, retaining every coordinate exactly.
