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jasperyeoh2/MD-trajectories-CPPF-tubulin-heterodimer-and-monomers

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-interactions — see docs/DIMER_TRAJECTORY_NAMING.md. What this dataset contains All-atom GROMACS production trajectories (.xtc) for CPPF with human tubulin: 5IJ0 / soluble curved dimer (main text): three heterodimer replicates extended to… See the full description on the dataset page: https://huggingface.co/datasets/jasperyeoh2/MD-trajectories-CPPF-tubulin-heterodimer-and-monomers.

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Dataset Card

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-interactions — see docs/DIMER_TRAJECTORY_NAMING.md.

What this dataset contains

All-atom GROMACS production trajectories (.xtc) for CPPF with human tubulin:

—5IJ0 / soluble curved dimer (main text): three heterodimer replicates extended to ~400 ns each.
—6E7B / lattice straight dimer (supplementary): three replicates × 200 ns each (no cofactors; comparable to main-text 5IJ0 setup).
—Monomers: six replicates (~200 ns each: α/β × three replicates).

Checksum sidecars: HF_UPLOAD_SHA256SUMS_all.txt, HF_UPLOAD_SHA256SUMS_dimer_extensions.txt, HF_UPLOAD_SHA256SUMS_6e7b.txt (uploads may be split 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).

6E7B supplementary trajectories (lattice straight state)

Reviewer-requested control matching the 6E7B microtubule-lattice-related conformation. No GTP/GDP/Mg²⁺ in the MD system (same cofactor-free protocol as main-text 5IJ0 for direct comparability).

Replicate	Hub filename	Typical on-disk path (`revision_exec_6e7b`)
rep1	`6e7b_rep1_md_200ns.xtc`	`md/rep1/md_200ns.xtc`
rep2	`6e7b_rep2_md_200ns.xtc`	`md/rep2/md_200ns.xtc`
rep3	`6e7b_rep3_md_200ns.xtc`	`md/rep3/md_200ns.xtc`

Paired run inputs (required to re-analyze `.xtc`):

Replicate	Hub filename	On-disk path
rep1	`6e7b_rep1_md_200ns.tpr`	`revision_exec_6e7b/md/rep1/md_200ns.tpr`
rep2	`6e7b_rep2_md_200ns.tpr`	`revision_exec_6e7b/md/rep2/md_200ns.tpr`
rep3	`6e7b_rep3_md_200ns.tpr`	`revision_exec_6e7b/md/rep3/md_200ns.tpr`

Last-50 ns subsampled trajectories (51 frames, MM-PBSA / lightweight re-analysis): 6e7b_rep{N}_md_200ns_last50ns_sub.xtc

Analysis outputs (plots, timeseries XVG, FEL): analysis_6e7b/ on this Hub. Scripts & topology mirror: revision_exec_6e7b/ on this Hub (production .xtc excluded; use flat names above).

Upload: revision_exec/scripts/huggingface_upload_6e7b_trajectories.sh --all then revision_exec/scripts/huggingface_upload_6e7b_reproducibility.sh --all

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).