FastMDXplora

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Software for automated molecular dynamics studies

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# FastMDXplora

**Molecular dynamics from a PDB code to a finished study — in one command.**

[![DOI](https://img.shields.io/badge/DOI-10.1002%2Fjcc.70350-blue?labelColor=black)](https://doi.org/10.1002/jcc.70350)
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[![OpenMM](https://img.shields.io/badge/engine-OpenMM-orange)](https://openmm.org)

[**Documentation**](https://fastmdxplora.readthedocs.io) ·
[**Quick start**](https://fastmdxplora.readthedocs.io/en/latest/getting_started.html) ·
[**GUI**](https://fastmdxplora.readthedocs.io/en/latest/gui.html) ·
[**Cite**](#citation)

</div>

---

```bash
fastmdx explore --system 181L
```

```
setup  →  simulation  →  analysis  →  report
```

Four characters of PDB ID as input. FastMDXplora fetches T4 lysozyme,
parameterises the benzene bound in its cavity, runs the dynamics, analyses the
trajectory, works out which residues hold the ligand in place, and writes the
whole study up as a PDF.

Or configure the whole MD study in the GUI:

```bash
fastmdx gui
```

## Install

```bash
conda create -n fastmdxplora -c conda-forge fastmdxplora
conda activate fastmdxplora
```

`fastmdx info` lists every backend and how to get anything missing:

```bash
fastmdx info
```

## What you can study

| | |
|---|---|
| **A protein on its own** | Fold, flexibility, secondary structure, native contacts, conformational clustering — from a PDB code. Fluctuations can be set against the crystal's own B-factors, and backbone order parameters against what NMR relaxation measures. |
| **A protein with a ligand** | The ligand is found, its chemistry resolved, its protonation settled in the binding site. Eight interaction types against published criteria tell you what *holds* it, not just what it touches. |
| **A membrane protein** | Embedded in one of seven bilayers, with the orientation checked rather than assumed and pressure coupling that suits a lipid system. |
| **Free energy along a coordinate** | Umbrella sampling, metadynamics and steered MD from a named collective variable — nine of them, one or two at a time — without writing PLUMED input. Each says what its output is and is not: a surface if the bias converged, a pathway and the work along it, a potential of mean force if the windows overlap. |
| **A trajectory from another engine** | Skip the simulation and analyse what you already have — GROMACS `.xtc` and `.trr`, Amber `.nc`, NAMD and CHARMM `.dcd`, LAMMPS `.lammpstrj`, or `.pdb`, `.cif` and `.h5` that carry their own topology. |
| **Many systems at once** | Mutants against wild type — named as `L99A`, and checked against the residue actually there — a sweep across a setting, runs pinned one per GPU, and a comparison report across all of them. Where the members differ only by seed, the spread of their means is set against the error each run claimed for itself. |

**It refuses rather than guesses.** An ambiguous ligand charge, a protein
backwards in its membrane, a free-energy surface that never converged — each
stops the run and is named, not papered over. Biased averages are corrected
to equilibrium where the bias allows and labelled where it does not. Every
step explains itself and cites the paper worth reading. What comes out, you
can defend; what you cannot is marked.

## The config is the study

A FastMDXplora config is the whole description of a molecular dynamics study:
the system, how it is prepared, how it is simulated, what is measured, and how
it is written up. Capture that, and the four phases — setup, simulation,
analysis, report — run themselves.

```yaml
systems:
  - system: 181L
simulation:
  duration_ns: 100
```

That is a complete study. Everything unnamed takes a documented default, and
every run writes `resolved_config.yml` with defaults, file and command line
merged, so the exact study can be run again by anyone holding that one file.

**Three ways to build a config**, and each of them also runs all four phases:

| | |
|---|---|
| **The GUI** | `fastmdx gui`. A form generated from the schema, so every system and every setting is reachable. Worth using even for a command-line or Python workflow: build the study where the options are visible and explained, then take the file away. |
| **The CLI** | `fastmdx explore --config study.yml`, or `fastmdx init-config` for a commented template, or a flag for any setting. |
| **The Python API** | `FastMDXplora(config="study.yml").explore()`, or the same blocks passed as options. |

None of these is the primary interface and none is a subset of another —
form, flags and API are generated from one declaration — and a study designed
in the GUI on a laptop runs unchanged on a cluster, because what travels is
the config.

## Documentation

**Start here** — [Install](https://fastmdxplora.readthedocs.io/en/latest/installation.html) ·
[Your first run](https://fastmdxplora.readthedocs.io/en/latest/getting_started.html) ·
[The GUI](https://fastmdxplora.readthedocs.io/en/latest/gui.html) ·
[The four phases](https://fastmdxplora.readthedocs.io/en/latest/phases.html)

**Going further** — [Restraints, membranes, enhanced sampling](https://fastmdxplora.readthedocs.io/en/latest/simulations.html) ·
[Production and GPUs](https://fastmdxplora.readthedocs.io/en/latest/production.html) ·
[Protein-ligand interactions](https://fastmdxplora.readthedocs.io/en/latest/interactions.html)

**Reference** — [CLI](https://fastmdxplora.readthedocs.io/en/latest/cli_reference.html) ·
[Configuration](https://fastmdxplora.readthedocs.io/en/latest/configuration.html) ·
[Examples](https://fastmdxplora.readthedocs.io/en/latest/usage_examples.html) ·
[Python API](https://fastmdxplora.readthedocs.io/en/latest/api.html)

## Citation

> Aina, A.; Kwan, D. *FastMDAnalysis: Software for Automated Analysis of Molecular Dynamics Trajectories.* J. Comput. Chem. **2026**, 47, e70350. DOI: [10.1002/jcc.70350](https://doi.org/10.1002/jcc.70350)

```bibtex
@article{aina2026fastmd,
  author  = {Aina, Adekunle and Kwan, Derrick},
  title   = {FastMDAnalysis: Software for Automated Analysis of Molecular Dynamics Trajectories},
  journal = {Journal of Computational Chemistry},
  volume  = {47},
  number  = {8},
  pages   = {e70350},
  year    = {2026},
  doi     = {10.1002/jcc.70350},
}
```

## Contributing

Contributions welcome — see [CONTRIBUTING.md](CONTRIBUTING.md). FastMDXplora
follows the [Contributor Covenant](CODE_OF_CONDUCT.md).

## License

MIT. See [LICENSE](LICENSE).

---

Built in the [AAI Research Lab](https://aai-research-lab.github.io) at
California State University Dominguez Hills, on MDTraj, OpenMM, PDBFixer,
OpenFF, RDKit, NumPy, SciPy, scikit-learn and Matplotlib.

</div>

FastMDXplora

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