| 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. | |