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:

fastmdx gui

Install

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

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

fastmdx info

What you can study

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, how it is analysed, and how it is written up. Capture that, and the four phases — setup, simulation, analysis, report — run themselves.

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 — the file, the command line and the API arguments 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:

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.

And a fourth, in place of a person. The FastMDXplora Agent writes a config from a sentence, and is reachable through all three of the above:

fastmdx agent "simulate trypsin with benzamidine bound at pH 6.5 for 100 ns"

It gets no special treatment. What it writes goes through exactly the same validator, by the same code, with the same refusals, as a config typed by hand — and a proposal that did not validate carries no config at all.

An AI app that speaks the Model Context Protocol reaches the same checks with fastmdx mcp: the AI app's model writes a study and the same validator judges it, it reads and compares studies, and it starts one only from a checked file, with your go-ahead.

The manifest is the result

What a config is to a study, manifest.json is to its result: every phase that ran, every artifact it produced, every setting it used, and the exact software stack it ran on — including which package versions were loaded, because those decide numbers. A run directory is readable by somebody who was not there.

Documentation

Start here — Install · Your first study · How FastMDXplora works

The Config — The FastMDXplora Config · Config reference · Selections · Examples

Writing a Config — GUI · CLI · API · Agent · From your AI app

Going further — Restraints, membranes, enhanced sampling · Production and GPUs · Running elsewhere

Results — The FastMDXplora Manifest · Reading the results · The analyses · Protein-ligand interactions · Refusals

For developers — Developing FastMDXplora · How it is validated

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

@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. Each contributor signs the Contributor License Agreement once. FastMDXplora follows the Contributor Covenant.

License

FastMDXplora is released under the MIT License. See LICENSE.