---
license: cc-by-4.0
language:
- en
tags:
- molecular-dynamics
- molecular-simulation
- peptides
- chemistry
- generative-modeling
pretty_name: Vacuum Peptide Trajectories
---

# Vacuum Peptide Ensembles

Molecular-dynamics trajectories derived from [ManyPeptidesMD](https://huggingface.co/datasets/transferable-samplers/many-peptides-md). This repository provides vacuum ensembles for a small subset of peptides, initialized from ManyPeptidesMD conformers.

## Overview

| Path | Model | Use |
| --- | --- | --- |
| `trajectories/v1/` | Amber14, peptide only | Gas-phase sampling |
| `webdatasets/v1/300K/` | Streamable samples from the 300 K state | Model training |
| `webdatasets/v1/300-500K/` | Streamable samples from all REMD states | Temperature-conditioned training |

Files follow:

```text
trajectories/v1/<split>/<length>/<sequence>/state_YY_<temperature>K.npz
```

Each NPZ contains `positions`, `smiles`, `id`, `temperature`, potential `energy`, and metadata. `positions` has shape `(frames, atoms, 4)` with rows `[atomic_number, x_nm, y_nm, z_nm]`.

Files aggregate independent REMD bursts initialized from up to 100 source conformers. Saved frames within each burst are 10 ps apart. Please note that the data were simulated using REMD, which breaks temporal ordering.

## Simulation

Starting structures came from the corresponding ManyPeptidesMD trajectories. Up to 100 conformers per sequence were selected by uniform stride from the end of each source trajectory. Peptide sequences, atom order, and train/validation/test assignments follow ManyPeptidesMD.

### Replica Exchange 

| Parameter | Value |
| --- | --- |
| Replicas | 8, geometrically spaced from 300 to 500 K |
| Temperatures | 300.00, 322.71, 347.14, 373.42, 401.69, 432.10, 464.81, 500.00 K |
| Integrator | Langevin, 2 fs, 0.3 ps^-1 collision rate |
| Warm-up / production | 0.5 ns / 100 ns per replica |
| Save interval | 5,000 steps = 10 ps |
| Exchange interval | 5,000 steps = 10 ps |

Outputs were demultiplexed by thermodynamic state. Each state file therefore represents a fixed temperature, not one replica's path through the ladder. Select `state_00_300p00K.npz` for 300 K data.

### Energy Function

- **Peptide:** Amber14.
- **Vacuum:** `NoCutoff`; H-bond constraints.

## Citation

Please cite this dataset and ManyPeptidesMD when using its peptide sequences or starting conformers:

```bibtex
@misc{rindtorff_2026_vacuum_peptide_trajectories,
  author       = {Rindtorff, Niklas},
  title        = {Vacuum Peptide Ensembles},
  year         = {2026},
  publisher    = {Hugging Face},
  howpublished = {\url{https://huggingface.co/datasets/niklastr/vacuum_peptides}},
  note         = {Dataset in progress; accessed 2026-07-23}
}

```

Source dataset: [ManyPeptidesMD](https://huggingface.co/datasets/transferable-samplers/many-peptides-md).

## License

This derived dataset is released under CC BY 4.0. ManyPeptidesMD is distributed under the terms stated in its [dataset repository](https://huggingface.co/datasets/transferable-samplers/many-peptides-md). See the source repository for authoritative terms and provenance caveats.