README.md

metadata

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.