---
license: mit
tags:
- molecular-dynamics
- openmm
- dipeptides
- ramachandran
- enhanced-sampling
size_categories:
- 10K<n<100K
---

# dipeptide-md-grid8-long

Long and grid-initialized MD trajectories for 4 capped dipeptides:
- `ala_ala`
- `ala_gly`
- `gly_gly`
- `gly_ala`

## Layout

- `long_trajectories/<molecule>/segment_70ns/`
- `long_trajectories/<molecule>/segment_130ns/`
- `grid_sampling/grid8_4d/common/`
- `grid_sampling/grid8_4d/<molecule>/{matches,metadata,init_structures}/`
- `grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/`

## Notes

- Long trajectories are produced at coordinate output frequency = 1 simulation step.
- `segment_130ns` are continuation trajectories from the corresponding 70ns runs.
- Grid data uses an `8x8x8x8` grid in 4 dihedral dimensions with periodic-distance matching.
- `metadata/source_paths.txt` records original source locations.