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PDB: revision_exec/prep/complex_start.pdb |
Total atoms: 7144 |
Chains: {'A': 3558, 'B': 3565, 'C': 21} |
Selected resnames counts: {'GTP': 32, 'MG': 1, 'GDP': 28} |
VALIDATION_STATUS: PASS |
PDB: revision_exec/prep/complex_start_clean.pdb |
Total atoms: 7144 |
Chains: {'A': 3558, 'B': 3565, 'C': 21} |
Selected resnames counts: {'GTP': 32, 'MG': 1, 'GDP': 28, 'CPP': 21} |
VALIDATION_STATUS: PASS |
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Check out the documentation for more information.
MD-trajectories-CPPF-tubulin-heterodimer-and-monomers
Copy this file into the Hugging Face dataset “README” (Dataset card).
Source of truth in Git: https://github.com/jasperyeoh/integrative-ai-assisted-modeling-of-cppf-tubulin-interaction-suggest-beta-tubulin-binding-preference — see docs/DIMER_TRAJECTORY_NAMING.md.
What this dataset contains
All-atom GROMACS production trajectories (.xtc) for CPPF with human tubulin: three heterodimer replicates (extended to ~400 ns per replicate) and six monomer replicates (~200 ns each: α/β × three replicates).
Checksum sidecars: HF_UPLOAD_SHA256SUMS_all.txt, HF_UPLOAD_SHA256SUMS_dimer_extensions.txt (commit may split uploads across bundles).
Important: dimer files named *_md_200ns.xtc are not “only 0–200 ns”
There is no missing 200–300 ns segment in the dimer data.
GROMACS often keeps the first output basename when the run is continued (checkpoint / append). The on-disk file is still called md_200ns.xtc, but the trajectory inside can run from ~0 to ~300 ns for the dimer. The next time windows are stored in the separate part files below.
| Approx. time (dimer) | What to use on this Hub (replicate in filename) | Typical on-disk name in the GitHub revision_exec tree |
|---|---|---|
| ~0 → 300 ns | dimer_rep{1,2,3}_md_200ns.xtc |
rep*/prod/md_200ns.xtc (name is legacy; content is not “200 ns only”) |
| ~300 → 350 ns | dimer_rep1_md_350ns.part0004.xtc or dimer_rep{2,3}_md_350ns.part0003.xtc |
md_350ns.part0004 (rep1) or md_350ns.part0003 (rep2/3) |
| ~350 → 400 ns | dimer_rep1_md_400ns.part0005.xtc or dimer_rep{2,3}_md_400ns.part0004.xtc |
matching md_400ns.part* |
Part indices differ between rep1 and rep2/3 because of how extensions were launched (-noappend, run numbering).
Monomers: monomer_*_md_200ns.xtc correspond to ~200 ns production per replicate (standard naming matches length).
Human-readable aliases (optional, Git repo only)
The GitHub repo may contain symlinks such as segment_0-300ns.xtc → md_200ns.xtc under revision_exec/rep*/prod/ (created by revision_exec/scripts/create_dimer_trajectory_symlinks.sh). These symlinks are not required on the Hub; they exist to avoid renaming canonical MD files that scripts and checkpoints rely on.
Workflow & environments
- Scripts and topology: same GitHub repo as above.
- Conda / GROMACS environment notes:
docs/CONDA_ENVIRONMENTS.md.
License
MIT (same as repository; confirm here matches your publication requirement).
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