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.

Run all four phases, or any one on its own — fastmdx setup, simulate, analyze, report. Each records what it did, so a run can be picked up, repeated or explained afterwards.

Or do the whole thing in the GUI:

fastmdx gui

The GUI is not a viewer bolted onto a command-line tool. Its form is generated from the same schema the CLI validates against, so every one of the hundred settings is reachable, every system FastMDXplora can study can be built there, and nothing can be configured in one interface and not the other. What it hands back is a config file — checked by the same validator before you ever see it — and fastmdx explore --config runs those same bytes on a laptop or a cluster. Build the study where it is convenient to think; run it where the compute is.

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, or a protein pointed the wrong way into a membrane, stops the run and gets named. A metadynamics run that crossed its barrier once when you asked for four gets no free energy surface. Averages from a biased trajectory are corrected back to equilibrium where the bias allows it, and labelled where it does not.

Every step says why it is happening, and cites the paper worth reading. What comes out is something you can defend — or is marked clearly as something you cannot.

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.

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:

A fourth way is to write the YAML by hand, which is short and readable enough that people do.

None of these is the primary interface and none is a subset of another. The form, the flags and the API are generated from one declaration of what the software can do, so a study you can express in one you can express in all of them. A study designed on a laptop in the GUI runs unchanged on a cluster from the command line, because what travels between them is the config.

Documentation

Start here — Install · Your first run · The GUI · The four phases

Going further — Restraints, membranes, enhanced sampling · Production and GPUs · Protein-ligand interactions

Reference — CLI · Configuration · Examples · Python API

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. FastMDXplora follows the Contributor Covenant.

License

MIT. See LICENSE.